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comparison access.xml @ 1:ae3ff7fd1efa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:34:55 +0000
parents 89362232bca6
children
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0:89362232bca6 1:ae3ff7fd1efa
2 <description>Calculate the sequence-accessible coordinates in chromosomes</description> 2 <description>Calculate the sequence-accessible coordinates in chromosomes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 #import re 10 #import re
10 ln -s '$fa_fname' ./genome.fasta && 11 ln -s '$fa_fname' ./genome.fasta &&
11 #if $exclude 12 #if $exclude
12 #set $names = [] 13 #set $names = []
13 #set $x=1 14 #set $x=1
14 #for $x, $exc in enumerate($exclude): 15 #for $x, $exc in enumerate($exclude):
15 #set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier) 16 #set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier)
16 #set $name = $name_base + '_' + str(x) 17 #set $name = $name_base
17 #silent $names.append( $name ) 18 #silent $names.append( $name )
18 ln -s '$exc' ${name}.bed && 19 ln -s '$exc' ${name}.bed &&
19 #end for 20 #end for
20 #end if 21 #end if
21 cnvkit.py access 22 cnvkit.py access
29 --min-gap-size $min_gap_size 30 --min-gap-size $min_gap_size
30 #end if 31 #end if
31 --output access-excludes.bed 32 --output access-excludes.bed
32 ]]></command> 33 ]]></command>
33 <inputs> 34 <inputs>
34 <param name="fa_fname" type="data" format="fasta" label="Target coverage file" help="Reference genome fasta file" /> 35 <param name="fa_fname" type="data" format="fasta" label="Genome FASTA file" help="Reference genome fasta file" />
35 <param argument="--min-gap-size" optional="true" type="integer" label="Minimum gap size between accessible sequence regions" min="0" value="5000" help="Regions separated by less than this distance will be joined together" /> 36 <param argument="--min-gap-size" optional="true" type="integer" label="Minimum gap size between accessible sequence regions" min="0" value="5000" help="Regions separated by less than this distance will be joined together" />
36 <param argument="--exclude" type="data" optional="true" format="bed" multiple="true" label="Additional regions to exclude" help="" /> 37 <param argument="--exclude" type="data" optional="true" format="bed" multiple="true" label="Additional regions to exclude" help="" />
37 </inputs> 38 </inputs>
38 <outputs> 39 <outputs>
39 <data name="out_sample_access" format="bed" label="${tool.name} on ${on_string}: Sequence-accessible coordinates" from_work_dir="access-excludes.bed" /> 40 <data name="out_sample_access" format="bed" label="${tool.name} on ${on_string}: Sequence-accessible coordinates" from_work_dir="access-excludes.bed" />