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annotate tools/cgatools17/fasta2crr.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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children 91e163b708d3
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1 <tool id="fasta2crr" name="fasta-2-crr" version="1.7.1">
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2 <description> Convert fasta sequences into a single reference crr file </description>
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3
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4 <requirements>
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5 <requirement type="package" version="1">cgatools17</requirement>
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6 </requirements>
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7
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8 <command>
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9 cgatools | head -1;
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10 cgatools fasta2crr
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11 #for $f in $fastafiles
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12 --input ${f.file}
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13 #end for
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14 --output $output
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15 #if $circ != "None"
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16 --circular $circ
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17 #end if
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18 </command>
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19
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20 <inputs>
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21 <repeat name="fastafiles" title="FASTA File" min="1">
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22 <param name="file" type="data" format="tsv" label="select input fasta file" />
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23 </repeat>
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24 <param name="circ" type="data" format="tsv,bz2" optional="true" label="select file containing comma-separated list of circular chromosome names"/>
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25 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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26 </inputs>
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27
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28 <outputs>
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29 <data format="crr" name="output" label="$fname ${tool.name} on ${on_string}"/>
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30 </outputs>
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31
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32 <help>
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33
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34 **What it does**
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35
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36 This tool converts input FASTA sequences into a single reference CRR file.
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37
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38 **cgatools 1.7.1 Documentation**
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39
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40 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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41
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42 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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43
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44 **Command line reference**::
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45
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46 COMMAND NAME
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47 fasta2crr - Converts fasta reference files to the crr format.
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48
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49 OPTIONS
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50 -h [ --help ]
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51 Print this help message.
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52
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53 --input arg
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54 The input fasta files (may be passed in as arguments at the end of the
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55 command, or omitted for stdin). Take care to specify the fasta files in
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56 chromosome order; ordering is important. To work with human Complete
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57 Genomics data, the chromosome order should be chr1...chr22, chrX, chrY,
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58 chrM.
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59
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60 --output arg
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61 The output crr file.
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62
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63 --circular arg
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64 A comma-separated list of circular chromosome names. If ommitted,
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65 defaults to chrM.
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66
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67 </help>
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68 </tool>
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69
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