Mercurial > repos > iuc > stacks2_denovomap

comparison stacks_denovomap.xml @ 1:afdbc7fcce70 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:17:15 -0400
parents b9822370f843
children 421c33b8bf17
comparison
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0:b9822370f843 1:afdbc7fcce70
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
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
12 #if $output_log
13 ln -s '$output_log' stacks_outputs/denovo_map.log &&
14 #end if
11 15
12 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" ) 16 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
13 $link_command 17 $link_command
14 18
15 denovo_map.pl 19 denovo_map.pl
33 37
34 ## the catalog.calls output is a gzip-ed vcf extract it 38 ## the catalog.calls output is a gzip-ed vcf extract it
35 ## to make it usable in Galaxy (with the downside that we 39 ## to make it usable in Galaxy (with the downside that we
36 ## need to gzip it again for downstream calls like populations) 40 ## need to gzip it again for downstream calls like populations)
37 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf 41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
38 && mv stacks_outputs/denovo_map.log $output_log
39 ]]></command> 42 ]]></command>
40 43
41 <inputs> 44 <inputs>
42 <expand macro="fastq_input"/> 45 <expand macro="fastq_input"/>
43 <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" />
159 <param name="popfilter_options|min_samples_per_pop" value="1"/> 162 <param name="popfilter_options|min_samples_per_pop" value="1"/>
160 <param name="popfilter_options|min_populations" value="0" /> 163 <param name="popfilter_options|min_populations" value="0" />
161 <assert_command> 164 <assert_command>
162 <has_text text="-M 3" /> 165 <has_text text="-M 3" />
163 <has_text text="-n 3" /> 166 <has_text text="-n 3" />
164 <has_text text="\-\-var-alpha 0.1" /> 167 <has_text text="--var-alpha 0.1" />
165 <has_text text="\-\-gt-alpha 0.1" /> 168 <has_text text="--gt-alpha 0.1" />
166 <has_text text="\-\-rm-pcr-duplicates" /> 169 <has_text text="--rm-pcr-duplicates" />
167 <has_text text="\-\-min-samples-per-pop 1" /> 170 <has_text text="--min-samples-per-pop 1" />
168 <has_text text="\-\-min-populations 0" /> 171 <has_text text="--min-populations 0" />
169 </assert_command> 172 </assert_command>
170 <output_collection name="tabs" count="6"/> 173 <output_collection name="tabs" count="6"/>
171 <output_collection name="catalog" type="list" count="3"/> 174 <output_collection name="catalog" type="list" count="3"/>
172 <output_collection name="matches" type="list" count="2"/> 175 <output_collection name="matches" type="list" count="2"/>
173 <output_collection name="bams" type="list" count="2"/> 176 <output_collection name="bams" type="list" count="2"/>