Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/crr2fasta.xml @ 15:b5c879e950f5 draft default tip

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 402ebee914f2286aa9d98223f501f06c1e4b9c22-dirty
author yhoogstrate
date Fri, 20 Nov 2015 03:50:36 -0500
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1 <tool id="crr2fasta" name="crr-2-fasta" 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 crr2fasta
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11 #if $refcrr.reference == "custom":
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12 --input $refcrr.customcrr
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13 #else:
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14 --input ${refcrr.reffile.fields.crr_path}
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15 #end if
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16 --output $output
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17 --line-width $linewidth
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18 </command>
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19
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20 <inputs>
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21 <conditional name="refcrr">
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22 <param name="reference" type="select" label="Reference">
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23 <option value="builtin" > Built-in Reference CRR </option>
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24 <option value="custom"> Custom CRR file </option>
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25 </param>
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26 <when value="builtin">
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27 <param name="reffile" type="select" label="Reference">
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28 <options from_data_table="cg_anno_files" />
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29 </param>
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30 </when>
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31 <when value="custom">
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32 <param name="customcrr" type="data" format="crr" label="Select custom crr file" />
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33 </when>
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34 </conditional>
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35
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36 <param name="linewidth" type="text" label="linewidth" size="15" value="50" />
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37 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="txt" name="output" label="$fname ${tool.name} on ${on_string}"/>
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42 </outputs>
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43
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44 <help>
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45
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46 **What it does**
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47
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48 This tool converts reference CRR files into the FASTA file format.
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49
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50 **cgatools 1.7.1 Documentation**
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51
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52 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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53
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54 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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55
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56 **Command line reference**::
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57
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58 COMMAND NAME
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59 crr2fasta - Converts a crr reference file to the fasta format.
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60
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61 OPTIONS
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62 -h [ --help ]
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63 Print this help message.
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64
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65 --input arg
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66 The input crr file (may be passed in as argument at the end of the
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67 command).
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68
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69 --output arg (=STDOUT)
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70 The output fasta file (may be omitted for stdout).
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71
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72 --line-width arg (=50)
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73 The maximum width of a line of sequence.
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74
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75
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76 </help>
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77 </tool>
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78
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79