standardize labels and extend tests

- add expect_num_outputs - standardize output labels
bernt-matthias · Nov 16, 2022 · 256b02d · 256b02d
1 parent 13fb031
commit 256b02d
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diff --git a/tools/rna_tools/locarna/locarna_exparnap.xml b/tools/rna_tools/locarna/locarna_exparnap.xml
@@ -203,45 +203,51 @@
     <outputs>
         <expand macro="standard_outupt" />
         <data format="ps" name="ps_fileA"
-              label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="ps" name="ps_fileB"
-              label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="txt" name="anchors_fasta"
-              label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
             <filter>'anchors-fasta' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppA"
-              label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppB"
-              label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="clustal" name="clustal"
-              label="${tool.name} chain as alignment (clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain as alignment (clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="tabular" name="epm_list"
-              label="${tool.name} list of epms on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms">
             <filter>'epm_list' in outputs</filter>
         </data>
         <data format="tabular" name="chained_epm_list"
-              label="${tool.name} list of epms in chain on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms in chain">
             <filter>'chained_epm_list' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="epm_list" />
             <output name="epm_list" file="tRNA_2.epms" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="LCSEPM preprocessing..."/>
+                    <has_text text="#EPMs:"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
 

diff --git a/tools/rna_tools/locarna/locarna_multiple.xml b/tools/rna_tools/locarna/locarna_multiple.xml
@@ -69,7 +69,7 @@
     #if 'clustal_strict' in str($outputs).split(",")
         && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
     #end if
-
+    && echo $outputs
     ]]></command>
 
     <inputs>
@@ -181,32 +181,58 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="max_diff_mode_selector" value="max-diff" />
             <param name="max_diff" value="20" />
+            <param name="outputs" value="clustal,clustal_strict"/>
             <output name="stdout" file="archaea-default.stdout" lines_diff="2" />
+            <output name="clustal">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="haca.snoRNA.fa" />
             <param name="stdout_verbosity" value="" />
             <output name="stdout" file="haca.snoRNA-default.stdout" lines_diff="2" />
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="alignment_mode_selector" value="probabilistic" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
             <output name="clustal" file="archaea-probabilistic.aln" lines_diff="2"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="max_diff_mode_selector" value="max-diff-aln" />
             <param name="max_diff_aln" value="archaea-ref.aln" />
             <param name="max_diff" value="2" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
             <output name="clustal" file="archaea-ref_result.aln" lines_diff="2"/>
         </test>
     </tests>

diff --git a/tools/rna_tools/locarna/locarna_pairwise.xml b/tools/rna_tools/locarna/locarna_pairwise.xml
@@ -182,31 +182,31 @@
     <outputs>
         <expand macro="standard_outupt" />
         <data format="clustal" name="clustal"
-              label="${tool.name} alignment (annotated clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="clustal" name="clustal_strict" 
-              label="${tool.name} alignment (clustal) on ${on_string}">
+              label="${tool.name}on ${on_string}: alignment (clustal)">
             <filter>'clustal_strict' in outputs</filter>
         </data>
         <data format="stockholm" name="stockholm"
-              label="${tool.name} alignment (stockholm) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
         <data format="txt" name="pp"
-              label="${tool.name} alignment (PP 2.0) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="clustal" />
             <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="haca.snoRNA-1.aln" />
             <param name="inputB" value="haca.snoRNA-2.aln" />
             <param name="outputs" value="clustal_strict,clustal" />

diff --git a/tools/rna_tools/locarna/locarna_pairwise_p.xml b/tools/rna_tools/locarna/locarna_pairwise_p.xml
@@ -141,7 +141,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="arc_match_probs,base_match_probs"/>

diff --git a/tools/rna_tools/locarna/locarna_reliability_profile.xml b/tools/rna_tools/locarna/locarna_reliability_profile.xml
@@ -141,25 +141,37 @@
 
     <outputs>
         <data format="pdf" name="pdf_output_plot"
-              label="${tool.name} reliability plot (pdf) ${on_string}">
+              label="${tool.name} on ${on_string}: plot">
             <filter>output_format == 'pdf'</filter>
         </data>
         <data format="png" name="png_output_plot"
-              label="${tool.name} reliability plot (png) ${on_string}">
+              label="${tool.name} on ${on_string}: plot">
             <filter>output_format == 'png'</filter>
         </data>
         <data format="txt" name="rscript_output"
-              label="${tool.name} reliability plot (R script) ${on_string}">
+              label="${tool.name} on ${on_string}: R script ">
             <filter> write_rscript is True </filter>
         </data>
-        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}" />
+        <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_archive" value="archaea.tar.gz" />
             <param name="write_rscript" value="true" />
+            <output name="pdf_output_plot">
+                <assert_contents>
+                    <has_text text="%PDF"/>
+                    <has_size value="5401" delta="100"/>
+                </assert_contents>
+            </output>
             <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="ONOFF"/>
+                    <has_text text="FIT"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
 

diff --git a/tools/rna_tools/locarna/macros.xml b/tools/rna_tools/locarna/macros.xml
@@ -291,33 +291,33 @@
     </xml>
 
     <xml name="standard_outupt">
-        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
+        <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">
             <filter>stdout_verbosity != '--quiet'</filter>
         </data>
     </xml>
 
     <xml name="mlocarna_outputs">
         <expand macro="standard_outupt" />
         <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
-              label="${tool.name} alignment (annotated clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="clustal" name="clustal_strict" 
               from_work_dir="mlocarna_results/results/result.strict-aln"
-              label="${tool.name} alignment (clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (clustal)">
             <filter>'clustal_strict' in outputs</filter>
         </data>
         <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
-              label="${tool.name} alignment (stockholm) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
         <data format="txt" name="pp"
               from_work_dir="mlocarna_results/results/result.pp"
-              label="${tool.name} alignment (PP 2.0) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
         <data format="tar.gz" name="mlocarna_results_tgz"
-              label="${tool.name} results archive on ${on_string}">
+              label="${tool.name} on ${on_string}: results archive">
             <filter>'mlocarna_results' in outputs</filter>
         </data>
     </xml>

diff --git a/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln b/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln
@@ -1,18 +1,11 @@
 CLUSTAL W --- LocARNA 1.9.0
 
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
-#A1                ............................................................
-#A2                ............................................................
-
-ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
-#A1                ....AAAAAA..................................................
-#A2                ....123456..................................................
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1                ................................................................AAAAAA..................................................
+#A2                ................................................................123456..................................................
 
 ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
 ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA

diff --git a/tools/rna_tools/locarna/test-data/haca.snoRNA.aln b/tools/rna_tools/locarna/test-data/haca.snoRNA.aln
@@ -1,14 +1,9 @@
 CLUSTAL W --- LocARNA 1.9.0
 
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
-
-ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
 
 ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
 ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA

diff --git a/tools/rna_tools/locarna/test-data/tRNA_2.aln b/tools/rna_tools/locarna/test-data/tRNA_2.aln
@@ -1,7 +1,4 @@
 CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875
 
-D10744             GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG
-AF008220           GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG
-
-D10744             UGAGUUCGAAUCUCACAUUUUCCG
-AF008220           GCGGUUCGAGCCCGUCAUCCUCCA
+D10744             GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+AF008220           GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCGGCGGUUCGAGCCCGUCAUCCUCCA