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comparison stacks_refmap.xml @ 5:466cc910d640 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
author matthias
date Wed, 27 Feb 2019 09:48:50 -0500
parents 93fb82c0fc94
children 60687cc87548
comparison
equal deleted inserted replaced
4:e1dbdd7175c8 5:466cc910d640
1 <tool id="stacks2_refmap" name="Stacks2: reference map" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_refmap" name="Stacks2: reference map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description> 2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="version_cmd"/>
8 <command><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @CLEAN_EXT@ 9 @FASTQ_INPUT_FUNCTIONS@
10 mkdir bam_inputs stacks_outputs&& 10 mkdir bam_inputs stacks_outputs&&
11 @BAM_INPUT@ 11 @BAM_INPUT@
12 12
13 ref_map.pl 13 ref_map.pl
14 --samples bam_inputs 14 --samples bam_inputs
15 #if str($popmap) != 'None': 15 #if str($popmap) != 'None':
16 --popmap '$popmap' 16 --popmap '$popmap'
17 #end if 17 #end if
18 $paired_select 18 $paired_select
19 -o stacks_outputs 19 -o stacks_outputs
20 -T \${GALAXY_SLOTS:-1} 20 -T \${GALAXY_SLOTS:-1}
21 --var-alpha $model_options.var_alpha 21 --var-alpha $model_options.var_alpha
22 --gt-alpha $model_options.gt_alpha 22 --gt-alpha $model_options.gt_alpha
23 23
24 && mv stacks_outputs/ref_map.log $output_log 24 @EXTRACT_VCF@
25
26 #if $output_log
27 && mv stacks_outputs/ref_map.log $output_log
28 #end if
25 ]]></command> 29 ]]></command>
26 30
27 <inputs> 31 <inputs>
28 <expand macro="bam_input_macro"/> 32 <expand macro="bam_input_macro"/>
29 <param argument="--popmap" type="data" format="tabular,txt" label="Population map" /> 33 <param argument="--popmap" type="data" format="tabular,txt" label="Population map" />
30 <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">
31 <option value="" selected="true">single/paired</option> 35 <option value="" selected="true">single/paired</option>
32 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> 36 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
33 <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>
34 </param> 38 </param>
35 <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">
48 <test> 52 <test>
49 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> 53 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
50 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 54 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
51 <param name="add_log" value="yes" /> 55 <param name="add_log" value="yes" />
52 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> 56 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
53 <!-- TODO test for outputs --> 57 <output_collection name="gstacks_out" type="list" count="2">
58 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
59 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
60 </output_collection>
61 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
62 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
63 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
64 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
65 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
66 <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/>
54 </test> 67 </test>
55 <test> 68 <test>
56 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> 69 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
57 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 70 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
58 <param name="paired_select" value="--unpaired"/> 71 <param name="paired_select" value="--unpaired"/>
63 <has_text text="--var-alpha 0.1" /> 76 <has_text text="--var-alpha 0.1" />
64 <has_text text="--gt-alpha 0.1" /> 77 <has_text text="--gt-alpha 0.1" />
65 </assert_command> 78 </assert_command>
66 <param name="add_log" value="yes" /> 79 <param name="add_log" value="yes" />
67 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> 80 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
81 <output_collection name="gstacks_out" type="list" count="2"/>
82 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
83 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
84 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
85 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
86 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
87 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
88
68 </test> 89 </test>
69 </tests> 90 </tests>
70 91
71 <help> 92 <help>
72 <![CDATA[ 93 <![CDATA[