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comparison small_rna_maps.xml @ 24:e75a10eba0a6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 0293b0f9b07302ba0b71e7877be1ea7a7ed04718
author artbio
date Sun, 31 Mar 2019 20:58:21 -0400
parents 3ca8113cc758
children 07aa8f928d4b
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23:3ca8113cc758 24:e75a10eba0a6
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.11.1"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.12.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
17 #import os 17 #import os
18 #for $file in $inputs 18 #for $file in $inputs
19 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' && 19 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
20 samtools index '$file.element_identifier' && 20 samtools index '$file.element_identifier' &&
21 #end for 21 #end for
22 ls -la ./ &&
23 python '$__tool_directory__'/small_rna_maps.py 22 python '$__tool_directory__'/small_rna_maps.py
24 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) } 23 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
25 #set $labels = list() 24 #set $labels = list()
26 #for $file in $inputs: 25 #for $file in $inputs:
27 $labels.append(str($file.element_identifier)) 26 $labels.append(str($file.element_identifier))