Mercurial > repos > iuc > stacks2_refmap

comparison stacks_refmap.xml @ 1:319b10947ec1 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 14:15:21 -0400
parents 45385ba40a75
children 6dafad990086
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0:45385ba40a75 1:319b10947ec1
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 bam_inputs stacks_outputs&& 10 mkdir bam_inputs stacks_outputs &&
11
12 #if $output_log
13 ln -s '$output_log' stacks_outputs/ref_map.log &&
14 #end if
15
11 @BAM_INPUT@ 16 @BAM_INPUT@
12 17
13 ref_map.pl 18 ref_map.pl
14 --samples bam_inputs 19 --samples bam_inputs
15 #if str($popmap) != 'None': 20 #if str($popmap) != 'None':
20 -T \${GALAXY_SLOTS:-1} 25 -T \${GALAXY_SLOTS:-1}
21 --var-alpha $model_options.var_alpha 26 --var-alpha $model_options.var_alpha
22 --gt-alpha $model_options.gt_alpha 27 --gt-alpha $model_options.gt_alpha
23 28
24 @EXTRACT_VCF@ 29 @EXTRACT_VCF@
25
26 #if $output_log
27 && mv stacks_outputs/ref_map.log $output_log
28 #end if
29 ]]></command> 30 ]]></command>
30 31
31 <inputs> 32 <inputs>
32 <expand macro="bam_input_macro"/> 33 <expand macro="bam_input_macro"/>
33 <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" />