Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 33:6fee74f6d2bd draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
author artbio
date Mon, 25 Oct 2021 09:21:34 +0000
parents f2e7ad3058e8
children 966bc5c46efd
comparison
equal deleted inserted replaced
32:f2e7ad3058e8 33:6fee74f6d2bd
1 <tool id="small_rna_maps" name="small_rna_maps" version="3.0.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="3.1.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.20.2=py38h9894fe3_0">numpy</requirement> 4 <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement>
5 <requirement type="package" version="0.16.0.1=py38hbdc2ae9_1">pysam</requirement> 5 <requirement type="package" version="0.17.0=py37h45aed0b_0">pysam</requirement>
6 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> 6 <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement>
7 <requirement type="package" version="0.6_29=r40h6115d3f_1">r-latticeextra</requirement> 7 <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement>
8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> 8 <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement>
9 <requirement type="package" version="1.4.4=r40h0357c0b_1">r-reshape2</requirement> 9 <requirement type="package" version="1.4.4=r40h03ef668_1">r-reshape2</requirement>
10 <requirement type="package" version="0.8.0=h984e79f_0">sambamba</requirement> 10 <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
11 <requirement type="package" version="1.10=h2e538c0_3">samtools</requirement>
12 <requirement type="package" version="68.1=h58526e2_0">icu</requirement> 11 <requirement type="package" version="68.1=h58526e2_0">icu</requirement>
13 </requirements> 12 </requirements>
14 <stdio> 13 <stdio>
15 <exit_code range="1:" level="fatal" description="Tool exception" /> 14 <exit_code range="1:" level="fatal" description="Tool exception" />
16 </stdio> 15 </stdio>
17 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
18 #import json 17 #import json
19 #import os 18 #import os
20 #for $file in $inputs 19 #for $file in $inputs
21 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' && 20 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
22 samtools index '$file.element_identifier' && 21 sambamba index -t \${GALAXY_SLOTS} '$file.element_identifier' &&
23 #end for 22 #end for
24 python '$__tool_directory__'/small_rna_maps.py 23 python '$__tool_directory__'/small_rna_maps.py
25 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) } 24 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
26 #set $labels = list() 25 #set $labels = list()
27 #for $file in $inputs: 26 #for $file in $inputs: