Mercurial > repos > iuc > stacks2_refmap
comparison stacks_refmap.xml @ 2:6dafad990086 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
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date | Thu, 16 Jul 2020 07:26:37 -0400 |
parents | 319b10947ec1 |
children | 4f65e343ecdf |
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1:319b10947ec1 | 2:6dafad990086 |
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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> |