Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/decodeCRR.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="cg_decodecrr" name="DecodeCRR" version="1.7.1">
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2
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3 <description>retreives the sequence for a given range of a chromosome.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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8
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9 <command>
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10 cgatools | head -1;
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11 cgatools decodecrr
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12 #if $refcrr.reference == "custom":
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13 --reference $refcrr.customcrr
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14 #else:
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15 --reference ${refcrr.reffile.fields.crr_path}
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16 #end if
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17 --output $output
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18 --range $range
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19 </command>
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20
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21 <inputs>
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22 <conditional name="refcrr">
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23 <param name="reference" type="select" label="Reference">
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24 <option value="builtin" > Built-in Reference CRR </option>
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25 <option value="custom"> Custom CRR file </option>
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26 </param>
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27 <when value="builtin">
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28 <param name="reffile" type="select" label="Reference">
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29 <options from_data_table="cg_anno_files" />
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30 </param>
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31 </when>
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32 <when value="custom">
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33 <param name="customcrr" type="data" format="crr" label="Select custom crr file" />
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34 </when>
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35 </conditional>
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36
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37 <param name="range" type="text" label="Select range" size="15" help="chr:begin-end e.g. chr4:30722030-30726957" />
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38 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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39 </inputs>
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40
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41 <outputs>
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42 <data format="txt" name="output" label="$fname ${tool.name} on ${on_string}"/>
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43 </outputs>
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44
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45 <help>
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46
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47 **What it does**
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48
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49 Retrieves the sequence for a given range of a chromosome.
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50
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51 **cgatools 1.7.1 Documentation**
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52
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53 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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54
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55 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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56
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57 **Command line reference**::
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58
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59 COMMAND NAME
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60 decodecrr - Prints the reference sequence for a given reference range.
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61
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62 OPTIONS
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63 -h [ --help ]
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64 Print this help message.
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65
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66 --reference arg
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67 The reference crr file (may be passed in as argument at the end of the
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68 command).
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69
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70 --output arg (=STDOUT)
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71 The output file (may be omitted for stdout).
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72
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73 --range arg
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74 The range of bases to print (chr,begin,end or chr:begin-end).
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75
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76 </help>
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77 </tool>
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78