Mercurial > repos > galaxyp > openms_rnpxlxicfilter

annotate RNPxlXICFilter.xml @ 13:8ee87d58ed48 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:53 +0000
parents 81d5ef72ef9d
children
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8128af6d94bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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2 <!--Proposed Tool Section: [Cross-Linking]-->
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3 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">RNPxlXICFilter</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir control &&
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17 cp '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
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18 mkdir treatment &&
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19 cp '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
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20 mkdir out &&
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22 ## Main program call
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24 set -o pipefail &&
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25 @EXECUTABLE@ -write_ctd ./ &&
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26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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28 -control
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29 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)'
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30 -treatment
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31 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)'
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32 -out
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33 'out/output.${gxy2omsext("mzml")}'
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35 ## Postprocessing
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36 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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38 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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39 #end if]]></command>
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40 <configfiles>
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41 <inputs name="args_json" data_style="paths"/>
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42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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43 </configfiles>
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44 <inputs>
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45 <param argument="-control" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
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46 <param argument="-treatment" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
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47 <param argument="-fold_change" type="float" value="2.0" label="fold change between XICs" help=""/>
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48 <param argument="-rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
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49 <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
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50 <expand macro="adv_opts_macro">
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51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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52 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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53 <expand macro="list_string_san" name="test"/>
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54 </param>
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55 </expand>
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56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test expect_num_outputs="1">
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68 <!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
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69 <param name="adv_opts|test" value="true"/>
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70 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
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71 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
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72 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
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73 </test>
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74 </tests>
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75 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment.
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77
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78 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlXICFilter.html]]></help>
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8a2e37503e3e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 <expand macro="references"/>
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4de461b0c05d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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80 </tool>