Mercurial > repos > computational-metabolomics > dimspy_get_peaklists

annotate get_peaklists.xml @ 0:afc9136ab094 draft

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:47:41 -0400
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afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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1 <tool id="dimspy_get_peaklists" name="Get peaklists" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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2 <description> or an average peaklist from a Peak Intensity Matrix</description>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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3 <macros>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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4 <import>macros.xml</import>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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5 </macros>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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6 <expand macro="requirements" />
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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7 <command detect_errors="exit_code">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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8 <![CDATA[
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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9 #if $input.format == 'all'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10 dimspy get-peaklists
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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11 #elif $input.format == 'average'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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12 dimspy get-average-peaklist
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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13 --name-peaklist '${input.name_peaklist}'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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14 #end if
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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15 --input '$hdf5_file_in'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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16 --output '$hdf5_file_out'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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17 #if $input.to_txt
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18 &&
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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19 dimspy hdf5-pls-to-txt
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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20 --input '$hdf5_file_out'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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21 --output .
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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22 --delimiter $delimiter
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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23 #end if
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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24 #if $input.format == 'average' and $input.to_txt
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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25 &&
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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26 mv '${input.name_peaklist}.txt' '$tsv_file_out'
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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27 #end if
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 ]]>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29 </command>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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30 <inputs>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" />
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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32 <conditional name="input">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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33 <param name="format" type="select" label="Get..." help="">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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34 <option value="average" selected="true">Average Peaklist</option>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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35 <option value="all">Multiple Peaklists (samples)</option>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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36 </param>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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37 <when value="average">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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38 <param name="name_peaklist" argument="--name-peaklist" type="text" value="" label="Name average Peaklist" >
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <validator type="empty_field" />
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 <validator type="regex" message="Value may include alphanumeric characters, underscores, dashes and spaces.">[A-Za-z0-9_\- ]+</validator>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 </param>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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42 <param name="to_txt" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Write Peaklists to tsv files (data collection)?" help=""/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 </when>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 <when value="all">
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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45 <param name="to_txt" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Write Peaklists to tsv files?" help=""/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 </when>
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47 </conditional>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" help=""/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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49 </inputs>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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50 <outputs>
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51 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)"/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
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53 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 <filter>input['to_txt'] is True</filter>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55 <filter>input['format'] == 'all'</filter>
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56 </collection>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 <data name="tsv_file_out" format="tsv" label="${tool.name} on ${on_string}: Average Peaklist">
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58 <filter>input['to_txt'] is True</filter>
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59 <filter>input['format'] == 'average'</filter>
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60 </data>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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61 </outputs>
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62 <tests>
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63 <test>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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64 <param name="format" value="all"/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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65 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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66 <param name="to_txt" value="True"/>
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67 <param name="delimiter" value="tab"/>
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68 <output_collection name="peaklists_txt" type="list">
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69 <element name="batch04_S01_rep01_247_2_248_3_249" file="batch04_S01_rep01_247_2_248_3_249.txt" ftype="tsv"/>
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70 </output_collection>
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71 </test>
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72 <test>
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73 <param name="format" value="average"/>
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74 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
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75 <param name="name_peaklist" value="batch04_S01_average"/>
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76 <param name="to_txt" value="True"/>
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77 <param name="delimiter" value="tab"/>
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78 <output name="tsv_file_out" file="batch04_S01_average.txt" ftype="tsv"/>
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79 </test>
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80 </tests>
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81 <help>
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82 -------------
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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83 Get Peaklists
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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84 -------------
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85
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86 ..
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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88 --------------------------------------
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90 Description
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91 -----------
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93 Use this tool to extract all individual peaklists, or an average of the individual peaklists, that were used in generating the input peak intensity matrix (.hdf5 format).
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95 --------------------------------------
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97 Parameters
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98 ----------
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100 |
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101
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102 **Peak Intensity Matrix (HDF5 file)** (REQUIRED) - a selection menu from which a specific peak intensity matrix (in .hdf5 format) can be selected from the active Galaxy history.
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104 |
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105
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106 **Get…** (REQUIRED; default **Average peaklist**) - a selection menu with options:
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107
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108 - **Average peaklist** - extract an intensity-averaged (non-weighted mean average and with NA values ignored) peaklist from the input peak intensity matrix. Averaging of intensities is performed across ALL samples included in the input peak intensity matrix (.hdf5 format).
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109
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110 **Name average peaklist** (REQUIRED if “average peaklist” selected; default = “'') - string indicating the name to append to the exported average peaklist (if any).
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111
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112 - **Multiple peaklists (samples)** - extract independent peaklists from the input .hdf5 file for each of the samples used in generating the peak intensity matrix.
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114 |
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116 **Write peaklists to tsv files (data collection)?** (REQUIRED; default = **Yes**) - binary toggle where:
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118 - **Yes** - corresponds to exporting peaklists(s) to the active Galaxy history in .tsv format
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120 - **No** - corresponds to skipping the export of peaklist(s) to the active Galaxy history in .tsv format
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122 |
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123
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124 **NOTE** - it is currently not possible to use the 'Write Peaklists to tsv files (data collection)?' option when selecting “Multiple Peaklists (samples)” from the “Get…” drop down menu.
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126 |
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130 Output file(s)
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131 --------------
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133 **Default output** - a .hdf5 file containing individual peaklists or an average peaklist.
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136 **Optional output** - peaklists (data collection), or an average peaklist, in .tsv format (tab-delimited text file) comprising a numeric data matrix (“.” as decimal, and NA for missing values). Each row corresponds to a peak detected in a specific file, or in the case of an average peaklist, a peak that was detected in AT LEAST one of the study samples. There is no filtering based on a minimum fraction of samples having a measured peak intensity value for a given peak. Columns provide metrics associated with each mass spectral peak. Metrics include:
afc9136ab094 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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138 @help_columns_peaklist@
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140 @example_peaklist@
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142 |
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144 --------------------------------------
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146 @github_developers_contributors@
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147 @license@
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148 </help>
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149 <expand macro="citations" />
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150 </tool>