Mercurial > repos > galaxyp > spectrast2spectrast_irt

annotate spectrast2spectrast_irt.xml @ 0:7b3c4703d81a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit d8b91dbe304c99bb5a46da25a5820005cde105c5-dirty
author galaxyp
date Sat, 30 May 2015 05:17:35 -0400
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0
7b3c4703d81a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit d8b91dbe304c99bb5a46da25a5820005cde105c5-dirty
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1 <tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.1.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.3.2">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 spectrast2spectrast_irt.py
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17 --in ${input}
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18 --out ./result_file.txt
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19 #if str($kit) != 'None':
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20 --kit "#echo ",".join(str($kit).split(','))#"
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21 #end if
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22 $applychauvenet
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23 $precursorlevel
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24 $spectralevel
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25 $report
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26 ##--exclude $exclude
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27 ##--surrogate $surrogate
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28 ##--linearregression $linearregression
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29 --rsq_threshold $rsq_threshold
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30
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="input" format="txt" type="data" label="Spectrast files" help="" />
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35
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36 <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False"
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37 label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" />
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38
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39 <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False"
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40 label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" />
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41
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42 <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False"
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43 label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" />
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44
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45 <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False"
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46 label="Create a report CSV file" help="(--report)" />
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47
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48 <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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49
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50 <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit">
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51 <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option>
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52 <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option>
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53 <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option>
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54 <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option>
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55 <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option>
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56 <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option>
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57 <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option>
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58 <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option>
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59 <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option>
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60 <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option>
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61 <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option>
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data format="txt" from_work_dir="result_file.txt" name="output_splib" />
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66 <data format="txt" from_work_dir="result_file.pepidx" name="output_pepidx" />
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67 <data format="txt" from_work_dir="result_file.csv" name="output_report">
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68 <filter>report</filter>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <!--
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73 <test>
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74 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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75 <param name="report" value="True" />
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76 <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" />
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77 <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" />
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78 <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" />
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79 </test>
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80 <test>
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81 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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82 <param name="report" value="False" />
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83 <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" />
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84 <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" />
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85 <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" />
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86 </test>
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87 -->
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88 </tests>
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89 <help>
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90 <![CDATA[
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91 **What it does**
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92
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93 Filter from spectraST files to swath input files.
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94
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95
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96 ]]>
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97 </help>
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98 <citations>
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99 </citations>
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100 </tool>