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comparison stacks_denovomap.xml @ 6:dddd1a6454ce draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:59:31 -0400
parents 3680074758c5
children
comparison
equal deleted inserted replaced
5:3680074758c5 6:dddd1a6454ce
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@ 9 @FASTQ_INPUT_FUNCTIONS@
10 mkdir stacks_inputs stacks_outputs&& 10 mkdir stacks_inputs stacks_outputs&&
11 11
12
13 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" ) 12 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
14 $link_command 13 $link_command
15 14
16 denovo_map.pl 15 denovo_map.pl
17 --samples stacks_inputs 16 --samples stacks_inputs
23 22
24 -M $assembly_options.M 23 -M $assembly_options.M
25 -n $assembly_options.n 24 -n $assembly_options.n
26 --var-alpha $model_options.var_alpha 25 --var-alpha $model_options.var_alpha
27 --gt-alpha $model_options.gt_alpha 26 --gt-alpha $model_options.gt_alpha
28 $paired 27 #if $input_type.input_type_select == "paired"
28 --paired
29 #end if
30 $pe_options.rm_pcr_duplicates
31 --min-samples-per-pop $popfilter_options.min_samples_per_pop
32 --min-populations $popfilter_options.min_populations
29 33
30 ## the catalog.calls output is a gzip-ed vcf extract it 34 ## the catalog.calls output is a gzip-ed vcf extract it
31 ## to make it usable in Galaxy (with the downside that we 35 ## to make it usable in Galaxy (with the downside that we
32 ## need to gzip it again for downstream calls like populations) 36 ## need to gzip it again for downstream calls like populations)
33 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf 37 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
39 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" /> 43 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
40 <section name="assembly_options" title="Assembly options" expanded="true"> 44 <section name="assembly_options" title="Assembly options" expanded="true">
41 <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"/> 45 <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"/>
42 <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"/> 46 <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"/>
43 </section> 47 </section>
44 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true"> 48 <section name="model_options" title="SNP model options" expanded="true">
45 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/> 49 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
46 </section> 50 </section>
47 <param argument="--paired" type="boolean" checked="false" truevalue="--paired" falsevalue="" label="Use paired-end reads to assemble mini-contigs" help="After assembling RAD loci (in the tsv2bam step)" /> 51 <section name="pe_options" title="Paired-end options" expanded="true">
52 <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="" />
53 </section>
54 <section name="popfilter_options" title="Population filtering options" expanded="true">
55 <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)"/>
56 <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)" />
57 </section>
48 <expand macro="in_log"/> 58 <expand macro="in_log"/>
49 </inputs> 59 </inputs>
50 <outputs> 60 <outputs>
51 <expand macro="out_log"/> <!-- pipeline also writes tsv2bam.log, gstacks.log, populations.log .. could be a collection --> 61 <expand macro="out_log"/> <!-- pipeline also writes tsv2bam.log, gstacks.log, populations.log .. could be a collection -->
52 <expand macro="ustacks_outputs_macro" tooladd="(ustacks)"/> 62 <expand macro="ustacks_outputs_macro" tooladd="(ustacks)"/>
80 </collection> 90 </collection>
81 </element> 91 </element>
82 </collection> 92 </collection>
83 </param> 93 </param>
84 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 94 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
85 <param name="paired" value="--paired" />
86 <output_collection name="tabs" count="6"> 95 <output_collection name="tabs" count="6">
87 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/> 96 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/>
88 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/> 97 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/>
89 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="2"/> 98 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="2"/>
90 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="2"/> 99 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="2"/>
144 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 153 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
145 <param name="assembly_options|M" value="3" /> 154 <param name="assembly_options|M" value="3" />
146 <param name="assembly_options|n" value="3" /> 155 <param name="assembly_options|n" value="3" />
147 <param name="model_options|var_alpha" value="0.1" /> 156 <param name="model_options|var_alpha" value="0.1" />
148 <param name="model_options|gt_alpha" value="0.1" /> 157 <param name="model_options|gt_alpha" value="0.1" />
158 <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates" />
159 <param name="popfilter_options|min_samples_per_pop" value="1"/>
160 <param name="popfilter_options|min_populations" value="0" />
149 <assert_command> 161 <assert_command>
150 <has_text text="-M 3" /> 162 <has_text text="-M 3" />
151 <has_text text="-n 3" /> 163 <has_text text="-n 3" />
152 <has_text text="\-\-var-alpha 0.1" /> 164 <has_text text="\-\-var-alpha 0.1" />
153 <has_text text="\-\-gt-alpha 0.1" /> 165 <has_text text="\-\-gt-alpha 0.1" />
166 <has_text text="\-\-rm-pcr-duplicates" />
167 <has_text text="\-\-min-samples-per-pop 1" />
168 <has_text text="\-\-min-populations 0" />
154 </assert_command> 169 </assert_command>
155 <output_collection name="tabs" count="6"/> 170 <output_collection name="tabs" count="6"/>
156 <output_collection name="catalog" type="list" count="3"/> 171 <output_collection name="catalog" type="list" count="3"/>
157 <output_collection name="matches" type="list" count="2"/> 172 <output_collection name="matches" type="list" count="2"/>
158 <output_collection name="bams" type="list" count="2"/> 173 <output_collection name="bams" type="list" count="2"/>
162 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output> 177 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
163 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> 178 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
164 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> 179 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
165 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output> 180 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
166 </test> 181 </test>
167 <!-- paired input, deafults (not using reverse reads), testing against the output of the pipeline components (note, this is equal because reverse reads are not used) -->
168 <test>
169 <param name="input_type|input_type_select" value="paired"/>
170 <param name="input_type|fqinputs">
171 <collection type="list:paired">
172 <element name="PopA_01">
173 <collection type="paired">
174 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
175 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
176 </collection>
177 </element>
178 <element name="PopA_02">
179 <collection type="paired">
180 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
181 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
182 </collection>
183 </element>
184 </collection>
185 </param>
186 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
187 <output_collection name="tabs" count="6"/>
188 <output_collection name="catalog" type="list" count="3"/>
189 <output_collection name="matches" type="list" count="2"/>
190 <output_collection name="bams" type="list" count="2"/>
191 <output_collection name="gstacks_out" type="list" count="2"/>
192 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
193 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
194 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
195 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
196 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
197 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
198 </test>
199 </tests> 182 </tests>
200 183
201 <help> 184 <help>
202 <![CDATA[ 185 <![CDATA[
203 .. class:: infomark 186 .. class:: infomark