Mercurial > repos > galaxyp > pepquery2_show_sets

annotate pepquery2_show_sets.xml @ 1:8671cf7c1671 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
author galaxyp
date Wed, 18 Oct 2023 06:40:48 +0000
parents b9e1e95758e8
children d39a43a076fc
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b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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1 <tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>PepQueryDB datasets, Parameters, PTMs</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 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 echo "PepQuery2 Show Sets $sets"
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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11 #if 'PepQueryDB_datasets' in $sets
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12 && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g' > '$pepquerydb'
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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13 #end if
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14 #if 'parameter_sets' in $sets
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15 && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters
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16 #end if
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17 #if 'printPTM' in $sets
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18 && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set">
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23 <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option>
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24 <option value="parameter_sets">PepQuery Predefined Parameter Sets</option>
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25 <option value="printPTM">PepQuery Modifications</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data name="pepquerydb" format="tabular" label="PepQueryDB datasets">
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30 <filter>'PepQueryDB_datasets' in sets</filter>
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31 <actions>
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32 <action name="comment_lines" type="metadata" default="1" />
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33 <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" />
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34 </actions>
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35 </data>
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36 <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets">
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37 <filter>'parameter_sets' in sets</filter>
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38 </data>
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39 <data name="ptm_list" format="tabular" label="PepQuery Modifications">
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40 <filter>'printPTM' in sets</filter>
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41 <actions>
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42 <action name="comment_lines" type="metadata" default="1" />
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43 <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" />
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44 </actions>
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45 </data>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <output name="pepquerydb">
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50 <assert_contents>
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51 <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57 **Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)*
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58
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59 @PEPQUERY_DOCUMANTATION_URL@
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60
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61 **PepQueryDB Datasets**
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62
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63 - Shows a table of all the indexed MS/MS datasets available in PepQueryDB.
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64 - *java -jar pepquery-2.0.2.jar -b show_full*
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65 - These datasets can be used for the **-b** option in **PepQuery**.
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66 - The parameter_set value can be used in the **-p** option in **PepQuery**.
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67 - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link
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68
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69
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70 **PepQuery Predefined Parameter Sets**
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71
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72 - Shows the predefined Parameter Set Names with the option settings
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73 - *java -jar pepquery-2.0.2.jar -p show*
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74 - The parameterset names can be used for the **-p** option in **PepQuery**.
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75
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76
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77 **PepQuery Modifications**
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79 - Shows a table of the PTMs available
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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80 - *java -jar pepquery-2.0.2.jar -printPTM*
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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81 - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**.
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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82 - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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83
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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84 ]]></help>
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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85 <expand macro="citations" />
b9e1e95758e8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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86 </tool>