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1 <tool id="rdata_2_out" name="RData cluster result to Text output" force_history_refresh="True">
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2 <command interpreter="python">rdata.2.out.py
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3 -d $dataset
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4 -f ${out_format.format}
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5
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6 #if str($out_format.format) == 'cls-only':
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7 -o ${output_cls}
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8 #end if
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9
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10 #if str($out_format.format) == 'newick':
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11 -o ${output_newick}
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12 #end if
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13
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14 #if str($out_format.format) == 'cdt':
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15 #if str($out_format.cdt_sec_dir_data) != "None":
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16 -D ${out_format.cdt_sec_dir_data}
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17 #end if
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18 -o ${output_cdt}
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19 -p ${output_cdt.files_path}
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20 #end if
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21
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22 #if str($out_format.format) == 'tabular':
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23 #if str($out_format.tab_sec_dir_data) != "None":
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24 -D ${out_format.tab_sec_dir_data}
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25 #end if
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26 -o ${output_tab}
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27 -p ${output_tab.files_path}
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28 #end if
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29
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30 </command>
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31 <inputs>
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32 <param name="dataset" type="data" format='rdata' label="Clustering Classification"/>
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33 <conditional name="out_format" >
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34 <param name="format" type="select" label="Select Output Format" >
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35 <option value="cls-only" selected='true'>Cluster Assignments Only</option>
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36 <option value="newick">Newick</option>
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37 <option value="cdt">TreeView (CDT)</option>
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38 <option value="tabular">Tab-delimited (all data, ordered by clusters)</option>
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39 </param>
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40 <when value='cdt'>
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41 <param name="cdt_sec_dir_data" type="data" format='rdata' label="Previous Cluster result #2 (secondary result, e.g. rows)" optional="true"/>
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42 </when>
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43 <when value='tabular'>
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44 <param name="tab_sec_dir_data" type="data" format='rdata' label="Previous Cluster result #2 (secondary result, e.g. rows)" optional="true"/>
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45 </when>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <data format="tabular" name="output_cls" label="Cluster Assignments Only (tab-delimited)" >
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50 <filter>(out_format['format']=="cls-only")</filter>
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51 </data>
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52 <data format="tgz" name="output_cdt" label="CDT File (tgz with CDT and ATR or GTR)" >
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53 <filter>(out_format['format']=="cdt")</filter>
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54 </data>
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55 <data format="tabular" name="output_newick" label="Newick File" >
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56 <filter>(out_format['format']=="newick")</filter>
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57 </data>
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58 <data format="tabular" name="output_tab" label="Tab-delimited File" >
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59 <filter>(out_format['format']=="tabular")</filter>
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60 </data>
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61 </outputs>
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62 <help>
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63 .. class:: infomark
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64
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65 **Convert RData file with cluster assignments and data to text (see below for text file options)** - Tool to convert a cluster assignment in tab-delimited format into an RData file format that can be read by the other tools in the Cluster-Tools Suite, e.g. The Kaplan-Meier Survival Plotting Tools
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66
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67
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68 **OUTPUT:** A new CDT file
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69
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70 ----
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71
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72 **Parameters**
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73
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74 - **Clustering Classification** Specify the clustering classification (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
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75 - **Select Output Format** Choice of the following
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76 * Cluster Assignments Only (2-column tab-delimited (ID-Cluster pairs)
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77 * Newick - dendrogram in Newick format
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78 * TreeView (CDT) - tarbal (tgz file) with requisite files (e.g. cdt, atr, gtr, jtv files)
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79 * Tab-delimited (all data, ordered by clusters)
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80
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81 - **IF Output Format is either TreeView or Tab-delimited (all data, ordered by clusters)**
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82 * **Previous Cluster result #2** Specify the clustering classification for the 2nd dimension (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
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83
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84
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85 </help>
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86 </tool>
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