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comparison ivar_removereads.xml @ 10:ee29337f905c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 8ce6fd9aee543d9e62db33a9c95f79d8dc4e6dea
author iuc
date Wed, 13 Jul 2022 15:20:33 +0000
parents 8d36959b000d
children 7f1cfa4c0e32
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9:8d36959b000d 10:ee29337f905c
1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy2"> 1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01">
2 <description>Remove reads from trimmed BAM file</description> 2 <description>Remove reads from trimmed BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
20 20
21 python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv && 21 python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv &&
22 ln -s '$input_bam' sorted.bam && 22 ln -s '$input_bam' sorted.bam &&
23 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && 23 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
24 24
25 ivar removereads 25 ivar removereads
26 -i sorted.bam 26 -i sorted.bam
27 -b binding_sites.bed 27 -b binding_sites.bed
28 -p removed_reads.bam 28 -p removed_reads.bam
29 -t masked_primers.txt 29 -t masked_primers.txt
30 ]]></command> 30 ]]></command>
107 .. class:: Warning mark 107 .. class:: Warning mark
108 108
109 Preprocessing of the BAM input with ivar trim is essential for this tool to 109 Preprocessing of the BAM input with ivar trim is essential for this tool to
110 work because only ``ivar trim`` can add required primer information to the 110 work because only ``ivar trim`` can add required primer information to the
111 BAM auxillary data of every read. 111 BAM auxillary data of every read.
112 112
113 ivar documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`__. 113 ivar documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`__.
114 ]]></help> 114 ]]></help>
115 <expand macro="citations" /> 115 <expand macro="citations" />
116 </tool> 116 </tool>