Mercurial > repos > iuc > stacks2_refmap
diff stacks_refmap.xml @ 2:6dafad990086 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
---|---|
date | Thu, 16 Jul 2020 07:26:37 -0400 |
parents | 319b10947ec1 |
children | 4f65e343ecdf |
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--- a/stacks_refmap.xml Mon Sep 30 14:15:21 2019 -0400 +++ b/stacks_refmap.xml Thu Jul 16 07:26:37 2020 -0400 @@ -31,7 +31,7 @@ <inputs> <expand macro="bam_input_macro"/> - <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" /> + <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/> <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"> <option value="" selected="true">single/paired</option> <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> @@ -50,42 +50,40 @@ <tests> <!-- bams as list --> - <test> + <test expect_num_outputs="7"> <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> - <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output> <output_collection name="gstacks_out" type="list" count="2"> - <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/> - <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/> + <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="4"/> + <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/> </output_collection> <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/> <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/> <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/> <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/> <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/> - <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/> </test> - <test> + <test expect_num_outputs="7"> <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> <param name="paired_select" value="--unpaired"/> - <param name="model_options|var_alpha" value="0.1" /> - <param name="model_options|gt_alpha" value="0.1" /> + <param name="model_options|var_alpha" value="0.1"/> + <param name="model_options|gt_alpha" value="0.1"/> <assert_command> - <has_text text="--unpaired" /> - <has_text text="--var-alpha 0.1" /> - <has_text text="--gt-alpha 0.1" /> + <has_text text="--unpaired"/> + <has_text text="--var-alpha 0.1"/> + <has_text text="--gt-alpha 0.1"/> </assert_command> - <param name="add_log" value="yes" /> - <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output> + <param name="add_log" value="yes"/> + <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output> <output_collection name="gstacks_out" type="list" count="2"/> <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output> <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output> <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output> <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output> </test> </tests> @@ -148,5 +146,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>