Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate get_length_and_gc_content.xml @ 10:f7f3f7db2d4a draft default tip

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author mvdbeek
date Thu, 31 Mar 2016 12:30:01 -0400
parents 0e9424413ab0
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1 <tool id="length_and_gc_content" name="gene length and gc content" version="0.1.0">
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2 <description>from GTF file</description>
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3 <macros>
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4 <import>go_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command interpreter="Rscript">
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9 get_length_and_gc_content.r --gtf "$gtf"
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10 #if $fastaSource.genomeSource == "indexed":
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11 --fasta "$fastaSource.fasta_pre_installed.fields.path"
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12 #else:
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13 --fasta "$fastaSource.fasta_history"
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14 #end if
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15 --length "$length"
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16 --gc_content "$gc_content"
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17 </command>
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18 <inputs>
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19 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" format="gtf" />
0
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20 <conditional name="fastaSource">
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21 <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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22 <option value="indexed">Use a built-in fasta</option>
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23 <option value="history">Use fasta from history</option>
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24 </param>
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25 <when value="indexed">
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26 <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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27 <options from_data_table="all_fasta"/>
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28 </param>
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29 </when>
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30 <when value="history">
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31 <param format="fasta" label="Select a fasta file that matches the supplied GTF file" name="fasta_history" type="data" />
0
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="tabular" label="gene length" name="length">
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37 <!-- future: set this when 16.04 has been released
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38 <actions>
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39 <action name="column_names" type="metadata" default="gene,length" />
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40 </actions>
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41 -->
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42 </data>
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43 <data format="tabular" label="gene gc content" name="gc_content">
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44 <!-- future: set this when 16.04 has been released
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45 <actions>
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46 <action name="column_names" type="metadata" default="gene,gc_content" />
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47 </actions>
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48 -->
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49 </data>
0
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50 </outputs>
6
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51 <tests>
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52 <test>
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53 <param name="gtf" value="in.gtf" ftype="gtf"></param>
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54 <param name="fastaSource|genomeSource" value="history"></param>
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55 <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
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56 <output name="length" file="length.tab"></output>
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57 <output name="gc_content" file="gc.tab"></output>
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58 </test>
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59 </tests>
0
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60 <help>
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61
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62 **What it does**
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63
6
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64 Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
0
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65
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66
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67 </help>
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68 <citations>
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69 </citations>
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70 </tool>