Mercurial > repos > iuc > stacks2_refmap

comparison stacks_refmap.xml @ 2:6e43ea81f086 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 21:13:59 +0000
parents e1f99efbfd81
children 3a6eacfb5ab6
comparison
equal deleted inserted replaced
1:e1f99efbfd81 2:6e43ea81f086
29 @EXTRACT_VCF@ 29 @EXTRACT_VCF@
30 ]]></command> 30 ]]></command>
31 31
32 <inputs> 32 <inputs>
33 <expand macro="bam_input_macro"/> 33 <expand macro="bam_input_macro"/>
34 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" /> 34 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
35 <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 <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">
36 <option value="" selected="true">single/paired</option> 36 <option value="" selected="true">single/paired</option>
37 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> 37 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
38 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option> 38 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
39 </param> 39 </param>
48 <expand macro="populations_output_light" tooladd="(populations)"/> 48 <expand macro="populations_output_light" tooladd="(populations)"/>
49 </outputs> 49 </outputs>
50 50
51 <tests> 51 <tests>
52 <!-- bams as list --> 52 <!-- bams as list -->
53 <test> 53 <test expect_num_outputs="7">
54 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> 54 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
55 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 55 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
56 <param name="add_log" value="yes" /> 56 <param name="add_log" value="yes"/>
57 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> 57 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output>
58 <output_collection name="gstacks_out" type="list" count="2"> 58 <output_collection name="gstacks_out" type="list" count="2">
59 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/> 59 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
60 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/> 60 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
61 </output_collection> 61 </output_collection>
62 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/> 62 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
63 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/> 63 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
64 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/> 64 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
65 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/> 65 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
66 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/> 66 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
67 <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/>
68 </test> 67 </test>
69 <test> 68 <test expect_num_outputs="7">
70 <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"/>
71 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 70 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
72 <param name="paired_select" value="--unpaired"/> 71 <param name="paired_select" value="--unpaired"/>
73 <param name="model_options|var_alpha" value="0.1" /> 72 <param name="model_options|var_alpha" value="0.1"/>
74 <param name="model_options|gt_alpha" value="0.1" /> 73 <param name="model_options|gt_alpha" value="0.1"/>
75 <assert_command> 74 <assert_command>
76 <has_text text="--unpaired" /> 75 <has_text text="--unpaired"/>
77 <has_text text="--var-alpha 0.1" /> 76 <has_text text="--var-alpha 0.1"/>
78 <has_text text="--gt-alpha 0.1" /> 77 <has_text text="--gt-alpha 0.1"/>
79 </assert_command> 78 </assert_command>
80 <param name="add_log" value="yes" /> 79 <param name="add_log" value="yes"/>
81 <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>
82 <output_collection name="gstacks_out" type="list" count="2"/> 81 <output_collection name="gstacks_out" type="list" count="2"/>
83 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output> 82 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
84 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output> 83 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
85 <output ftype="txt" name="out_populations_log_distribs"><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>
86 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> 85 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
87 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> 86 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
88 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
89 87
90 </test> 88 </test>
91 </tests> 89 </tests>
92 90
93 <help> 91 <help>
146 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 144 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
147 145
148 @STACKS_INFOS@ 146 @STACKS_INFOS@
149 ]]> 147 ]]>
150 </help> 148 </help>
151 <expand macro="citation" /> 149 <expand macro="citation"/>
152 </tool> 150 </tool>