Mercurial > repos > jjohnson > spectrast2spectrast_irt

annotate spectrast2spectrast_irt.xml @ 1:dc40297705fc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit 616f0282d3a3e0b433c324e899bea7b0dcd3d7e0-dirty
author jjohnson
date Thu, 26 Jul 2018 10:53:48 -0400
parents 90dcbb52c83a
children f5ca880950f7
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90dcbb52c83a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit 225dd7d91b12108dd3a4eec00e45771ec8127259-dirty
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1 <tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.5.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.5.0">msproteomicstools</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 ## may have to link splib
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17 mkdir -p outdir &&
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18 spectrast2spectrast_irt.py
1
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19 --in ${input.extra_files_path}/library.sptxt
0
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20 --out outdir/library.splib
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21 #if str($kit) != 'None':
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22 --kit "#echo ",".join(str($kit).split(','))#"
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23 #end if
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24 $applychauvenet
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25 $precursorlevel
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26 $spectralevel
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27 $report
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28 ##--exclude $exclude
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29 ##--surrogate $surrogate
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30 ##--linearregression $linearregression
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31 --rsq_threshold $rsq_threshold &&
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32 cp -p outdir/library.splib outdir/library.sptxt &&
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33 mkdir -p '$output.files_path' &&
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34 for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param name="input" format="splib" type="data" label="Spectrast files" help="" />
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39
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40 <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False"
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41 label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" />
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42
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43 <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False"
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44 label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" />
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45
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46 <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False"
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47 label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" />
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48
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49 <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False"
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50 label="Create a report CSV file" help="(--report)" />
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51
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52 <param name="rsq_threshold" type="float" value="0.95" label="Specify r-squared threshold to accept linear regression" help="(--rsq_threshold)" />
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53
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54 <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit">
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55 <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option>
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56 <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option>
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57 <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option>
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58 <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option>
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59 <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option>
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60 <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option>
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61 <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option>
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62 <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option>
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63 <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option>
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64 <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option>
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65 <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option>
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66 </param>
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67 </inputs>
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68 <outputs>
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69 <data name="output_report" format="csv" from_work_dir="outdir/library.csv">
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70 <filter>report</filter>
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71 </data>
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72 <data name="output" format="splib"/>
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73 </outputs>
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74 <tests>
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75 <!--
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76 <test>
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77 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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78 <param name="report" value="True" />
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79 <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" />
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80 <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" />
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81 <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" />
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82 </test>
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83 <test>
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84 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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85 <param name="report" value="False" />
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86 <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" />
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87 <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" />
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88 <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" />
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89 </test>
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90 -->
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91 </tests>
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92 <help>
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93 <![CDATA[
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94 **What it does**
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95
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96 Filter from spectraST files to swath input files.
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97
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98
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99 ]]>
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100 </help>
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101 <citations>
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102 </citations>
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103 </tool>