annotate riboplot.xml @ 7:096c6bbf4a04

Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Thu, 13 Aug 2015 15:03:20 +0100
parents 1901dcdc12ff
children 844eb8c36f32
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1 <tool id="riboplot" name="riboplot" version="0.1.0">
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2 <description>Plot and output read counts for a single transcript in an alignment (BAM)
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.2.1">matplotlib</requirement>
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6 <requirement type="package" version="0.8.3">pysam</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error" />
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10 </stdio>
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11 <command interpreter="python">riboplot/riboplot.py
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12 --ribo_file "${ribo_file}"
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13 --transcriptome_fasta "${transcriptome_fasta}"
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14 --transcript_name "${transcript_name}"
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15 #if $rnacov.rnacov_select=="yes"
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16 --rna_file "${rna_file}"
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17 #end if
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18 --read_length "${read_length}"
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19 --read_offset "${read_offset}"
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20 --html_file "${html_file}"
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21 --output_path "${html_file.files_path}"
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22 ## --debug
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23 </command>
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24 <inputs>
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25 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
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26 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
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27 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
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28 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
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29 <validator type="empty_field" message="Field requires a value"/>
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30 <sanitizer>
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31 <valid>
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32 <add value="|"/>
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33 </valid>
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34 </sanitizer>
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35 </param>
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36 <conditional name="rnacov">
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37 <param name="rnacov_select" type="select" label="Include RNA Coverage">
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38 <option value="no">No</option>
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39 <option value="yes">Yes</option>
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40 </param>
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41 <when value="yes">
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42 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
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43 </when>
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44 <when value="no" />
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45 </conditional>
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46 <param name="read_length" type="integer" label="Read length to consider" value="28"/>
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47 <param name="read_offset" type="integer" label="Offset" value="0"/>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="html_file" label="riboplot (HTML report)"/>
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51 </outputs>
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52 <help>
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53 </help>
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54 </tool>