Mercurial > repos > artbio > small_rna_maps
diff small_rna_maps.xml @ 33:6fee74f6d2bd draft
"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 |
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--- a/small_rna_maps.xml Sun May 09 17:11:00 2021 +0000 +++ b/small_rna_maps.xml Mon Oct 25 09:21:34 2021 +0000 @@ -1,14 +1,13 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="3.0.0"> +<tool id="small_rna_maps" name="small_rna_maps" version="3.1.0"> <description></description> <requirements> - <requirement type="package" version="1.20.2=py38h9894fe3_0">numpy</requirement> - <requirement type="package" version="0.16.0.1=py38hbdc2ae9_1">pysam</requirement> - <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> - <requirement type="package" version="0.6_29=r40h6115d3f_1">r-latticeextra</requirement> - <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> - <requirement type="package" version="1.4.4=r40h0357c0b_1">r-reshape2</requirement> - <requirement type="package" version="0.8.0=h984e79f_0">sambamba</requirement> - <requirement type="package" version="1.10=h2e538c0_3">samtools</requirement> + <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement> + <requirement type="package" version="0.17.0=py37h45aed0b_0">pysam</requirement> + <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement> + <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement> + <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement> + <requirement type="package" version="1.4.4=r40h03ef668_1">r-reshape2</requirement> + <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement> <requirement type="package" version="68.1=h58526e2_0">icu</requirement> </requirements> <stdio> @@ -19,7 +18,7 @@ #import os #for $file in $inputs sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' && - samtools index '$file.element_identifier' && + sambamba index -t \${GALAXY_SLOTS} '$file.element_identifier' && #end for python '$__tool_directory__'/small_rna_maps.py --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }