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author mvdbeek
date Fri, 26 Feb 2016 13:26:56 -0500
parents 1b03f6232900
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1 <tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0">
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2 <description />
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3 <requirements>
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4 <requirement type="package" version="3.2.1">R</requirement>
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5 <requirement type="package" version="1.22.0">goseq</requirement>
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6 </requirements>
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7 <command interpreter="Rscript">
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8 get_length_and_gc_content.r --gtf "$gtf"
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9 #if $fastaSource.genomeSource == "indexed":
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10 --fasta "$fastaSource.fasta_pre_installed.fields.path"
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11 #else:
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12 --fasta "$fastaSource.fasta_history"
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13 #end if
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14 --output "$output"
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15 </command>
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16 <inputs>
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17 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" />
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18 <conditional name="fastaSource">
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19 <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
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20 <option value="indexed">Use a built-in fasta</option>
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21 <option value="history">Use fasta from history</option>
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22 </param>
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23 <when value="indexed">
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24 <param help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence" name="fasta_pre_installed" type="select">
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25 <options from_data_table="all_fasta"/>
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26 </param>
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27 </when>
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28 <when value="history">
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29 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" />
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data format="tabular" label="length and gc content" name="output" />
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35 </outputs>
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36 <tests></tests>
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37 <help>
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39 **What it does**
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41 Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file.
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44 </help>
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45 <citations>
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46 </citations>
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47 </tool>