diff call.xml @ 2:9946bd542898 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"

--- a/call.xml	Thu Oct 29 20:50:39 2020 +0000
+++ b/call.xml	Fri Jan 22 14:31:44 2021 +0000
@@ -35,89 +35,84 @@
 #if 'dump' in $oo.out
     --dump 'dump.tsv.gz'
 #end if
-## samples
-#for $i, $current in enumerate($samples)
-    'sample_${i}.bam'
+## input
+#for $i, $current in enumerate($input)
+    'input_${i}.bam'
 #end for
 
 ## postprocessing
 @LOG@
+@DUMP@
 @VCF@
-@DUMP@
     ]]></command>
     <inputs>
-        <expand macro="samples"/>
+        <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/>
         <section name="generic" title="Generic options" expanded="true">
             <expand macro="svtype"/>
             <expand macro="genome"/>
             <expand macro="exclude"/>
         </section>
         <section name="discovery" title="Discovery options" expanded="true">
-            <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/>
-            <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
+            <param name="mapqual" type="integer" value="1" label="Set minimum paired-end mapping quality" help="(--map-qual)"/>
+            <param name="qualtra" type="integer" value="20" label="Set minimum paired-end quality for translocation" help="(--qual-tra)"/>
             <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
             <expand macro="minclip"/>
             <expand macro="mincliquesize"/>
-            <expand macro="minrefsep"/>
-            <expand macro="maxreadsep"/>
+            <expand macro="minrefsep" default="25"/>
+            <expand macro="maxreadsep" default="40"/>
         </section>
         <section name="genotyping" title="Genotyping options" expanded="true">
             <expand macro="vcffile"/>
             <expand macro="genoqual"/>
         </section>
-        <section name="oo" title="Output options">
+        <section name="oo" title="Output options" expanded="true">
             <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
                 <option value="bcf" selected="true">BCF</option>
-                <option value="vcf">VCF</option>
+                <option value="log">Log</option>
                 <option value="dump">SV-reads (--dump)</option>
-                <option value="log">Log</option>
+                <option value="vcf">VCF</option>
             </param>
         </section>
     </inputs>
     <outputs>
-        <expand macro="vcf"/>
         <expand macro="bcf"/>
         <expand macro="dump"/>
         <expand macro="log"/>
+        <expand macro="vcf"/>
     </outputs>
     <tests>
         <!-- no test implemented for parameter vcffile -->
 
         <!-- #1 default, single -->
         <test expect_num_outputs="2">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="genome" value="genome.fasta"/>
             </section>
             <section name="oo">
                 <param name="out" value="vcf,bcf"/>
             </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1184" delta="10"/>
+                </assert_contents>
+            </output>
             <output name="out_vcf">
                 <assert_contents>
                     <has_size value="3661" delta="10"/>
                     <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
                 </assert_contents>
             </output>
-            <output name="out_bcf">
-                <assert_contents>
-                    <has_size value="1184" delta="10"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- #2 default, multi; test data to small, results are empty -->
         <test expect_num_outputs="3">
-            <param name="samples" value="normal.bam,tumor.bam"/>
+            <param name="input" value="normal.bam,tumor.bam"/>
             <section name="generic">
                 <param name="genome" value="genome.fasta"/>
             </section>
             <section name="oo">
                 <param name="out" value="vcf,bcf,log"/>
             </section>
-            <output name="out_vcf">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
             <output name="out_bcf">
                 <assert_contents>
                     <has_size value="0"/>
@@ -128,10 +123,15 @@
                     <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
                 </assert_contents>
             </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
         </test>
-       <!-- #3; results are empty due to exclude file -->
+        <!-- #3; results are empty due to exclude file -->
         <test expect_num_outputs="4">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="genome" value="genome.fasta"/>
                 <param name="exclude" value="exclude.tsv"/>
@@ -139,11 +139,6 @@
             <section name="oo">
                 <param name="out" value="vcf,bcf,dump,log"/>
             </section>
-            <output name="out_vcf">
-                <assert_contents>
-                    <has_size value="0"/>
-                </assert_contents>
-            </output>
             <output name="out_bcf">
                 <assert_contents>
                     <has_size value="0"/>
@@ -159,10 +154,15 @@
                     <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
                 </assert_contents>
             </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- #4 -->
         <test expect_num_outputs="1">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="svtype" value="ALL"/>
                 <param name="genome" value="genome.fasta"/>
@@ -191,7 +191,7 @@
         </test>
         <!-- #5 -->
         <test expect_num_outputs="1">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="svtype" value="DEL"/>
                 <param name="genome" value="genome.fasta"/>
@@ -207,7 +207,7 @@
         </test>
         <!-- #6 -->
         <test expect_num_outputs="1">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="svtype" value="INS"/>
                 <param name="genome" value="genome.fasta"/>
@@ -223,7 +223,7 @@
         </test>
         <!-- #7 -->
         <test expect_num_outputs="1">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="svtype" value="INV"/>
                 <param name="genome" value="genome.fasta"/>
@@ -239,7 +239,7 @@
         </test>
         <!-- #8 -->
         <test expect_num_outputs="2">
-            <param name="samples" value="normal.bam"/>
+            <param name="input" value="normal.bam"/>
             <section name="generic">
                 <param name="svtype" value="BND"/>
                 <param name="genome" value="genome.fasta"/>
@@ -269,11 +269,11 @@
 
 **Input**
 
-Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
+Delly *call* requires a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a BCF/VCF file for genotyping can be applied.
 
 **Output**
 
-The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided.
+The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided.
 
 .. class:: infomark