Mercurial > repos > jjohnson > mzsqlite_psm_align

comparison mzsqlite_psm_align.xml @ 5:af5f22779a8e draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
author jjohnson
date Tue, 10 Apr 2018 11:52:04 -0400
parents a96b2754171c
children 100cff4db790
comparison
equal deleted inserted replaced
4:a96b2754171c 5:af5f22779a8e
5 <requirement type="package">twobitreader</requirement> 5 <requirement type="package">twobitreader</requirement>
6 <requirement type="package">pysam</requirement> 6 <requirement type="package">pysam</requirement>
7 <requirement type="package">gffutils</requirement> 7 <requirement type="package">gffutils</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #if $readlignments:
11 ln -s -f '${$readlignments}' 'input.bam' &&
12 ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' &&
13 #end if
10 python '$__tool_directory__/mzsqlite_psm_align.py' 14 python '$__tool_directory__/mzsqlite_psm_align.py'
11 #if $ref.ref_source == 'cached': 15 #if $ref.ref_source == 'cached':
12 --twobit='$ref.ref_loc.fields.path' 16 --twobit='$ref.ref_loc.fields.path'
13 #elif $ref.ref_source == 'history': 17 #elif $ref.ref_source == 'history':
14 --twobit='$ref.ref_file' 18 --twobit='$ref.ref_file'
15 #end if 19 #end if
16 #if $gffutilsdb: 20 #if $gffutilsdb:
17 --gffutils_file '$gffutilsdb' 21 --gffutils_file '$gffutilsdb'
18 #end if 22 #end if
19 #if $readlignments: 23 #if $readlignments:
20 --reads_bam '$readlignments' 24 --reads_bam 'input.bam'
21 #end if 25 #end if
22 #if 'probed' in str($output_formats).split(','): 26 #if 'probed' in str($output_formats).split(','):
23 --probed '$probed' 27 --probed '$probed'
24 #end if 28 #end if
25 #if 'prosam' in str($output_formats).split(','): 29 #if 'prosam' in str($output_formats).split(','):
60 <option value="prosam">pro.sam</option> 64 <option value="prosam">pro.sam</option>
61 <option value="probed">pro.bed</option> 65 <option value="probed">pro.bed</option>
62 </param> 66 </param>
63 </inputs> 67 </inputs>
64 <outputs> 68 <outputs>
65 <data name="prosam" format="sam"> 69 <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
66 <filter>'prosam' in output_formats</filter> 70 <filter>'prosam' in output_formats</filter>
67 </data> 71 </data>
68 <data name="probam" format="pro.bam"> 72 <data name="probam" format="bam" label="pro.Bam on ${on_string}">
69 <filter>'probam' in output_formats</filter> 73 <filter>'probam' in output_formats</filter>
70 </data> 74 </data>
71 <data name="probed" format="pro.bed"> 75 <data name="probed" format="bed" label="pro.Bed on ${on_string}">
72 <filter>'probed' in output_formats</filter> 76 <filter>'probed' in output_formats</filter>
73 </data> 77 </data>
74 </outputs> 78 </outputs>
75 <help><![CDATA[ 79 <help><![CDATA[
76 80