Mercurial > repos > iuc > stacks2_denovomap

comparison stacks_denovomap.xml @ 2:421c33b8bf17 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 17:25:36 -0400
parents afdbc7fcce70
children ad5ab22ffe24
comparison
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1:afdbc7fcce70 2:421c33b8bf17
41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf 41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
42 ]]></command> 42 ]]></command>
43 43
44 <inputs> 44 <inputs>
45 <expand macro="fastq_input"/> 45 <expand macro="fastq_input"/>
46 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" /> 46 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
47 <section name="assembly_options" title="Assembly options" expanded="true"> 47 <section name="assembly_options" title="Assembly options" expanded="true">
48 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/> 48 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
49 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/> 49 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
50 </section> 50 </section>
51 <section name="model_options" title="SNP model options" expanded="true"> 51 <section name="model_options" title="SNP model options" expanded="true">
52 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/> 52 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
53 </section> 53 </section>
54 <section name="pe_options" title="Paired-end options" expanded="true"> 54 <section name="pe_options" title="Paired-end options" expanded="true">
55 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help="" /> 55 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help=""/>
56 </section> 56 </section>
57 <section name="popfilter_options" title="Population filtering options" expanded="true"> 57 <section name="popfilter_options" title="Population filtering options" expanded="true">
58 <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/> 58 <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/>
59 <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)" /> 59 <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)"/>
60 </section> 60 </section>
61 <expand macro="in_log"/> 61 <expand macro="in_log"/>
62 </inputs> 62 </inputs>
63 <outputs> 63 <outputs>
64 <expand macro="out_log"/> <!-- pipeline also writes tsv2bam.log, gstacks.log, populations.log .. could be a collection --> 64 <expand macro="out_log"/> <!-- pipeline also writes tsv2bam.log, gstacks.log, populations.log .. could be a collection -->
74 <!-- paired input using also reverse reads, 74 <!-- paired input using also reverse reads,
75 the results are tested for equality, the tools corresponding the the programs 75 the results are tested for equality, the tools corresponding the the programs
76 used in the pipeline have also a test (should be the first) that test for 76 used in the pipeline have also a test (should be the first) that test for
77 equality thereby it is "ensured" that the pipeline w defaults is doing the same 77 equality thereby it is "ensured" that the pipeline w defaults is doing the same
78 as the components w defaults. --> 78 as the components w defaults. -->
79 <test> 79 <test expect_num_outputs="11">
80 <param name="input_type|input_type_select" value="paired"/> 80 <param name="input_type|input_type_select" value="paired"/>
81 <param name="input_type|fqinputs"> 81 <param name="input_type|fqinputs">
82 <collection type="list:paired"> 82 <collection type="list:paired">
83 <element name="PopA_01"> 83 <element name="PopA_01">
84 <collection type="paired"> 84 <collection type="paired">
85 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 85 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
86 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> 86 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
87 </collection> 87 </collection>
88 </element> 88 </element>
89 <element name="PopA_02"> 89 <element name="PopA_02">
90 <collection type="paired"> 90 <collection type="paired">
91 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 91 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
92 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> 92 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
93 </collection> 93 </collection>
94 </element> 94 </element>
95 </collection> 95 </collection>
96 </param> 96 </param>
97 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 97 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
98 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
98 <output_collection name="tabs" count="6"> 99 <output_collection name="tabs" count="6">
99 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/> 100 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/>
100 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/> 101 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/>
101 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="2"/> 102 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/>
102 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="2"/> 103 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/>
103 <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="2"/> 104 <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/>
104 <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="2"/> 105 <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/>
105 </output_collection> 106 </output_collection>
106 <output_collection name="catalog" type="list" count="3"> 107 <output_collection name="catalog" type="list" count="3">
107 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> 108 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/>
108 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> 109 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/>
109 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> 110 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/>
110 </output_collection> 111 </output_collection>
111 <output_collection name="matches" type="list" count="2"> 112 <output_collection name="matches" type="list" count="2">
112 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/> 113 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
113 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/> 114 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
114 </output_collection> 115 </output_collection>
115 <output_collection name="bams" type="list" count="2"> 116 <output_collection name="bams" type="list" count="2">
116 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/> 117 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
117 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size" /> 118 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
118 </output_collection> 119 </output_collection>
119 <output_collection name="gstacks_out" type="list" count="2"> 120 <output_collection name="gstacks_out" type="list" count="2">
120 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/> 121 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
121 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/> 122 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
122 </output_collection> 123 </output_collection>
123 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> 124 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
124 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="sim_size"/> 125 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="sim_size" delta_frac="0.01"/>
125 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" compare="sim_size"/> 126 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
126 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> 127 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
127 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv" compare="sim_size"/> 128 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
128 <output ftype="tabular" name="out_sql" value="populations/populations.markers.tsv"/>
129 </test> 129 </test>
130 <!-- SE input as multi selection, defaults testing against the output of the pipeline components --> 130 <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
131 <test> 131 <test expect_num_outputs="11">
132 <param name="input_type|input_type_select" value="single"/> 132 <param name="input_type|input_type_select" value="single"/>
133 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> 133 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
134 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 134 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
135 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
135 <output_collection name="tabs" count="6"/> 136 <output_collection name="tabs" count="6"/>
136 <output_collection name="catalog" type="list" count="3"/> 137 <output_collection name="catalog" type="list" count="3"/>
137 <output_collection name="matches" type="list" count="2"/> 138 <output_collection name="matches" type="list" count="2"/>
138 <output_collection name="bams" type="list" count="2"/> 139 <output_collection name="bams" type="list" count="2"/>
139 <output_collection name="gstacks_out" type="list" count="2"/> 140 <output_collection name="gstacks_out" type="list" count="2"/>
140 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output> 141 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
141 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output> 142 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
142 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output> 143 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
143 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> 144 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
144 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> 145 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
145 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
146 </test> 146 </test>
147 <!-- SE input as list, non-defaults, testing only correct size of the collections --> 147 <!-- SE input as list, non-defaults, testing only correct size of the collections -->
148 <test> 148 <test expect_num_outputs="11">
149 <param name="input_type|input_type_select" value="paired"/> 149 <param name="input_type|input_type_select" value="paired"/>
150 <param name="input_type|fqinputs"> 150 <param name="input_type|fqinputs">
151 <collection type="list"> 151 <collection type="list">
152 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 152 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
153 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> 153 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
154 </collection> 154 </collection>
155 </param> 155 </param>
156 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 156 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
157 <param name="assembly_options|M" value="3" /> 157 <param name="assembly_options|M" value="3"/>
158 <param name="assembly_options|n" value="3" /> 158 <param name="assembly_options|n" value="3"/>
159 <param name="model_options|var_alpha" value="0.1" /> 159 <param name="model_options|var_alpha" value="0.1"/>
160 <param name="model_options|gt_alpha" value="0.1" /> 160 <param name="model_options|gt_alpha" value="0.1"/>
161 <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates" /> 161 <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
162 <param name="popfilter_options|min_samples_per_pop" value="1"/> 162 <param name="popfilter_options|min_samples_per_pop" value="1"/>
163 <param name="popfilter_options|min_populations" value="0" /> 163 <param name="popfilter_options|min_populations" value="0"/>
164 <assert_command> 164 <assert_command>
165 <has_text text="-M 3" /> 165 <has_text text="-M 3"/>
166 <has_text text="-n 3" /> 166 <has_text text="-n 3"/>
167 <has_text text="--var-alpha 0.1" /> 167 <has_text text="--var-alpha 0.1"/>
168 <has_text text="--gt-alpha 0.1" /> 168 <has_text text="--gt-alpha 0.1"/>
169 <has_text text="--rm-pcr-duplicates" /> 169 <has_text text="--rm-pcr-duplicates"/>
170 <has_text text="--min-samples-per-pop 1" /> 170 <has_text text="--min-samples-per-pop 1"/>
171 <has_text text="--min-populations 0" /> 171 <has_text text="--min-populations 0"/>
172 </assert_command> 172 </assert_command>
173 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
173 <output_collection name="tabs" count="6"/> 174 <output_collection name="tabs" count="6"/>
174 <output_collection name="catalog" type="list" count="3"/> 175 <output_collection name="catalog" type="list" count="3"/>
175 <output_collection name="matches" type="list" count="2"/> 176 <output_collection name="matches" type="list" count="2"/>
176 <output_collection name="bams" type="list" count="2"/> 177 <output_collection name="bams" type="list" count="2"/>
177 <output_collection name="gstacks_out" type="list" count="2"/> 178 <output_collection name="gstacks_out" type="list" count="2"/>
178 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output> 179 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
179 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output> 180 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
180 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output> 181 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
181 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> 182 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
182 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> 183 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
183 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
184 </test> 184 </test>
185 </tests> 185 </tests>
186 186
187 <help> 187 <help>
188 <![CDATA[ 188 <![CDATA[
242 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 242 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
243 243
244 @STACKS_INFOS@ 244 @STACKS_INFOS@
245 ]]> 245 ]]>
246 </help> 246 </help>
247 <expand macro="citation" /> 247 <expand macro="citation"/>
248 </tool> 248 </tool>