Mercurial > repos > matthias > stacks2_denovomap

diff stacks_denovomap.xml @ 5:3680074758c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:14:41 -0400
parents a70c766ce64f
children dddd1a6454ce
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line diff
--- a/stacks_denovomap.xml	Wed Feb 27 09:55:08 2019 -0500
+++ b/stacks_denovomap.xml	Thu Jun 20 08:14:41 2019 -0400
@@ -36,13 +36,13 @@
 
     <inputs>
         <expand macro="fastq_input"/>
-        <param argument="--popmap" type="data" format="tabular,txt" label="Population map" />
+        <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
         <section name="assembly_options" title="Assembly options" expanded="true">
             <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
             <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
         </section>
         <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
-            <expand macro="variant_calling_options_vg"/>
+            <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
         </section>
         <param argument="--paired" type="boolean" checked="false" truevalue="--paired" falsevalue="" label="Use paired-end reads to assemble mini-contigs" help="After assembling RAD loci (in the tsv2bam step)" />
         <expand macro="in_log"/>
@@ -105,7 +105,7 @@
                 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size"  />
             </output_collection>
             <output_collection name="gstacks_out" type="list" count="2">
-                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf"/>
+                <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
                 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
             </output_collection>
             <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>