Mercurial > repos > malex > secimtools
annotate modify_design_file.xml @ 1:2e7d47c0b027 draft
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author | malex |
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date | Mon, 08 Mar 2021 22:04:06 +0000 |
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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_modify_design_file" name="Modify design file" version="@WRAPPER_VERSION@"> |
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2 <description>to remove specified group types or sampleIDs</description> |
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3 <macros> |
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4 <import>macros.xml</import> |
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5 </macros> |
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6 <expand macro="requirements" /> |
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7 <command><![CDATA[ |
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8 modify_design_file.py |
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9 --input $input |
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10 --design $design |
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11 --uniqID $uniqID |
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12 #if $group |
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13 --group $group |
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14 #end if |
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15 --drops $toDrop |
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16 --out $out |
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17 ]]></command> |
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18 <inputs> |
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19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/> |
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20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/> |
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21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/> |
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22 <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/> |
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23 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s) or Sample(s), comma separated, to remove from your design file."/> |
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24 </inputs> |
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25 <outputs> |
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26 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/> |
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27 </outputs> |
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28 <tests> |
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29 <test> |
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30 <param name="input" value="ST000006_data.tsv"/> |
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31 <param name="design" value="ST000006_design_group_name_underscore.tsv"/> |
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32 <param name="uniqID" value="Retention_Index" /> |
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33 <param name="group" value="White_wine_type_and_source_no_space" /> |
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34 <param name="toDrop" value="Chardonnay_Napa_CA2003,Riesling_CA2004,SauvignonBlanc_LakeCounty_CA2001" /> |
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35 <output name="out" file="ST000006_modify_design_output.tsv" /> |
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36 </test> |
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37 </tests> |
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38 <help><![CDATA[ |
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39 |
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40 @TIP_AND_WARNING@ |
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41 |
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42 **Tool Description** |
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43 |
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44 The tool creates a new design file based on the existing wide dataset and design file where the specified group types or samples are removed from the existing design file. |
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45 |
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46 -------------------------------------------------------------------------------- |
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47 |
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48 **Input** |
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49 |
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50 - Two input datasets are required. |
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51 |
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52 @WIDE@ |
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53 |
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54 **NOTE:** The sample IDs must match the sample IDs in the Design File |
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55 (below). Extra columns will automatically be ignored. |
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56 |
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57 @METADATA@ |
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58 |
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59 @UNIQID@ |
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60 |
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61 **Group/Treatment [Optional]** |
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62 |
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63 - Name of the column in your Design File that contains group classifications. If not provided, the drop will be performed by 'sampleID's. |
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64 |
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65 **Group(s)/Sample(s) to drop** |
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66 |
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67 - Name of the Group(s) or Sample(s), comma separated, to remove from the design file. |
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68 |
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69 -------------------------------------------------------------------------------- |
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70 |
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71 **Output** |
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72 |
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73 This tool will output a single design file that contains only the samples not selected for removal. |
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74 |
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75 ]]></help> |
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76 <expand macro="citations"/> |
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77 </tool> |