Mercurial > repos > iuc > cnvkit_batch

diff batch.xml @ 2:0d371963d4b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
author iuc
date Fri, 13 Dec 2024 23:53:57 +0000
parents 0c60bd0f4de6
children 004311c34527
line wrap: on
line diff
--- a/batch.xml	Fri Sep 29 15:28:46 2023 +0000
+++ b/batch.xml	Fri Dec 13 23:53:57 2024 +0000
@@ -147,16 +147,20 @@
     </outputs>
     <tests>
         <test expect_num_outputs="13">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="history"/>
-                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            <conditional name="CNV_reference">
+                <conditional name="reference_source">
+                    <param name="ref_selector" value="history"/>
+                    <param name="fasta" ftype="fasta" value="genome.fasta" />
+                </conditional>
+                <param name="CNV_reference_availabel" value="no" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="targets" ftype="bed" value="capture.bed" />
             </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="normal" ftype="bam" value="normal.bam" />
-            <param name="targets" ftype="bed" value="capture.bed" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
@@ -176,7 +180,9 @@
             <output name="out_capture_antitarget" file="capture.antitarget.bed" />
             <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
             <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-            <output name="out_reference_cnn" file="reference.cnn" />
+            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
+            </output>
             <output name="out_capture_target">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>
@@ -188,16 +194,20 @@
             </output>
         </test>
         <test expect_num_outputs="13">
-            <conditional name="reference_source">
-                <param name="ref_selector" value="cached"/>
-                <param name="fasta" value="test_buildid"/>
+            <conditional name="CNV_reference">
+                <conditional name="reference_source">
+                    <param name="ref_selector" value="cached"/>
+                    <param name="fasta" value="test_buildid"/>
+                </conditional>
+                <param name="CNV_reference_availabel" value="no" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="targets" ftype="bed" value="capture.bed" />
             </conditional>
-            <param name="CNV_reference_availabel" value="no" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="normal" ftype="bam" value="normal.bam" />
-            <param name="targets" ftype="bed" value="capture.bed" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
@@ -217,7 +227,9 @@
             <output name="out_capture_antitarget" file="capture.antitarget.bed" />
             <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
             <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-            <output name="out_reference_cnn" file="reference.cnn" />
+            <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+                <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
+            </output>
             <output name="out_capture_target">
                 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
             </output>
@@ -229,11 +241,15 @@
             </output>
         </test>
         <test expect_num_outputs="10">
-            <param name="CNV_reference_availabel" value="yes" />
-            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
-            <param name="reference" ftype="tabular" value="reference.cnn" />
-            <param name="scatter" value="1"/>
-            <param name="diagram" value="1"/>
+            <conditional name="CNV_reference">
+                <param name="CNV_reference_availabel" value="yes" />
+                <param name="input_sample_file" ftype="bam" value="tumor.bam" />
+                <param name="reference" ftype="tabular" value="reference.cnn" />
+            </conditional>
+            <section name="output_section">
+                <param name="scatter" value="1"/>
+                <param name="diagram" value="1"/>
+            </section>
             <output name="out_sample_bintest" file="tumor.bintest.cns" />
             <output name="out_sample_antitargetcoverage">
                 <assert_contents><has_text text="chromosome"/></assert_contents>