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comparison stacks_refmap.xml @ 6:60687cc87548 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 08:11:14 -0400
parents 466cc910d640
children
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5:466cc910d640 6:60687cc87548
28 #end if 28 #end if
29 ]]></command> 29 ]]></command>
30 30
31 <inputs> 31 <inputs>
32 <expand macro="bam_input_macro"/> 32 <expand macro="bam_input_macro"/>
33 <param argument="--popmap" type="data" format="tabular,txt" label="Population map" /> 33 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
34 <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input"> 34 <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input">
35 <option value="" selected="true">single/paired</option> 35 <option value="" selected="true">single/paired</option>
36 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> 36 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
37 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option> 37 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
38 </param> 38 </param>
39 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true"> 39 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
40 <expand macro="variant_calling_options_vg"/> 40 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
41 </section> 41 </section>
42 <expand macro="in_log"/> 42 <expand macro="in_log"/>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <expand macro="out_log"/> <!-- pipeline also writes other logs? .. could be a collection --> 45 <expand macro="out_log"/> <!-- pipeline also writes other logs? .. could be a collection -->