Mercurial > repos > jackcurragh > ribogalaxy_create_ribosome_profile

comparison create_ribosome_profile/create_ribosome_profile.xml @ 4:49e8fcbaaa72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Wed, 18 May 2022 11:57:34 +0000
parents dfed3b7be399
children 4d69f7428243
comparison
equal deleted inserted replaced
3:dfed3b7be399 4:49e8fcbaaa72
1 <tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.a"> 1 <tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
2 <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description> 2 <description>Produce a sorted bed file of A-Site profiles of RPFs.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.73">biopython</requirement> 4 <requirement type="package" version="1.79">biopython</requirement>
5 <requirement type="package" version="0.19.0">pysam</requirement> 5 <requirement type="package" version="0.19.0">pysam</requirement>
6 </requirements> 6 </requirements>
7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4} ${output1}</command> 7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} $refGenomeSource.genomeSource
8 #if $refGenomeSource.genomeSource == "builtin":
9 none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
10 #else:
11 ${refGenomeSource.input1_file} none ${input4} ${output1}
12 #end if
13 </command>
8 <inputs> 14 <inputs>
9 <param name="input1" type="data" format="bam" label="BAM file to process"/> 15 <param name="input1" type="data" format="bam" label="BAM file to process"/>
10 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/> 16 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
17 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
18 <option value="builtin">Use a built-in FASTA</option>
19 <option value="history">Use one from the history</option>
20 </param>
21 <when value="builtin">
22 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
23 <options from_data_table="builtin_fastas">
24 <filter type="sort_by" column="2" />
25 <validator type="no_options" message="No built-ins are available" />
26 </options>
27 </param>
28 </when>
29 <when value="history">
30 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
31 </when>
11 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/> 32 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
12 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase"> 33 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
13 <option value="offset" selected="true">Use offset approach</option> 34 <option value="offset" selected="true">Use offset approach</option>
14 <option value="weight">Use weight centered approach</option> 35 <option value="weight">Use weight centered approach</option>
15 </param> 36 </param>