Mercurial > repos > computational-metabolomics > dimspy_align_samples

annotate align_samples.xml @ 2:7b6f148bd99f draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:57:52 +0000
parents c72868b80c29
children
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7b6f148bd99f "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
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1 <tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy1">
0
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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2 <description> - Align peaks across Peaklists</description>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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3 <macros>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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4 <import>macros.xml</import>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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5 </macros>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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6 <expand macro="requirements" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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7 <command detect_errors="exit_code">
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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8 <![CDATA[
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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9 dimspy align-samples
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10 --input '$hdf5_file_in'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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11 --output '$hdf5_file_out'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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12 #if $filelist
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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13 --filelist '$filelist'
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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14 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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15 --ppm $ppm
2
7b6f148bd99f "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
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16 --ncpu \${GALAXY_SLOTS:-1}
7b6f148bd99f "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
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17 --block-size $adv.block_size
0
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18 #if $hdf5_to_txt.standard
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19 &&
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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20 @HDF5_PM_TO_TXT@
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21 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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22 #if $hdf5_to_txt.comprehensive
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23 &&
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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24 @HDF5_PM_TO_TXT_COMPREHENSIVE@
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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25 #end if
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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26 ]]>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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27 </command>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 <inputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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30 <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for Process Scans or Replicate Filter." />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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32 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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33 <expand macro="hdf5_pm_to_txt" />
2
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34 <section name="adv" title="Advanced options" expanded="False">
7b6f148bd99f "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
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35 <param name="block_size" argument="--block-size" type="integer" value="5000" label="Block size" help="The size of each block of peaks to perform clustering on." />
7b6f148bd99f "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
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36 </section>
0
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37 </inputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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38 <outputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <expand macro="outputs_peak_intensity_matrix" />
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 </outputs>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 <tests>
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42 <test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 <param name="ppm" value="2.0"/>
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45 <param name="delimiter" value="tab"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 <conditional name="hdf5_to_txt" >
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47 <param name="standard" value="True"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 <param name="comprehensive" value="False"/>
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49 <param name="samples_representations" value="rows"/>
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50 <param name="matrix_attr" value="intensity"/>
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51 </conditional>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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53 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 </test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55 <test>
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56 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 <param name="ppm" value="2.0"/>
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58 <param name="delimiter" value="tab"/>
2
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59 <conditional name="hdf5_to_txt" >
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60 <param name="standard" value="True"/>
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61 <param name="comprehensive" value="False"/>
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62 <param name="samples_representations" value="rows"/>
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63 <param name="matrix_attr" value="intensity"/>
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64 </conditional>
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65 <section name="adv">
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66 <param name="block_size" value="10000"/>
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67 </section>
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68 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
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69 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
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70 </test>
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71 <test>
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72 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
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73 <param name="ppm" value="2.0"/>
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74 <param name="delimiter" value="tab"/>
0
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75 <conditional name="hdf5_to_txt">
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76 <param name="standard" value="True"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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77 <param name="comprehensive" value="False"/>
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78 <param name="representation_samples" value="columns"/>
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79 <param name="matrix_attr" value="intensity"/>
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80 </conditional>
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81 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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82 <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv"/>
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83 </test>
33b65dacd377 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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84 <test>
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85 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
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86 <param name="ppm" value="2.0"/>
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87 <param name="delimiter" value="tab"/>
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88 <conditional name="hdf5_to_txt">
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89 <param name="standard" value="True"/>
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90 <param name="comprehensive" value="True"/>
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91 <param name="samples_representations" value="rows"/>
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92 <param name="matrix_attr" value="mz"/>
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93 </conditional>
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94 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
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95 <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv"/>
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96 <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv"/>
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97 </test>
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98 </tests>
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99 <help>
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100 -------------
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101 Align Samples
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102 -------------
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103
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104 ..
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105
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106 -------------------------------
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107
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108 Description
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109 -----------
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110
1
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111 Standard DIMS processing workflow: Process Scans -> [Replicate Filter] -> **Align Samples** -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics
0
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112
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113 |
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114
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115 This tool takes the peaklists for all study samples and merges them in to single aligned peak matrix. The peak matrix comprises a table, with samples along one axis and the mass-to-charge ratios of detected mass spectral peaks along the opposite axis. At the intersection of sample and mass-to-charge ratio, the intensity is given for a specific peak in a specific sample (if no intensity recorded, then ‘0’ is inserted).
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116
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117 -------------------------------
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118
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119 Parameters
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120 ----------
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121
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122 **Peaklists (HDF5 file)** (REQUIRED) - a HDF5 file containing all peaklists to undergo alignment.
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123
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124 |
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125
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126 **Filelist / Samplelist** (REQUIRED) - a file of type ‘tabular’ with the following required columns (additional metadata columns may also be included, e.g. “collectionTime”, etc.):
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127
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128 - **filename** - the name of the .raw or .mzML files from which peaklists were extracted using the “Process Scans” tool
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129
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130 - **batch** - a numeric value indicating the analysis batches samples were analysed in (if a single large analytica run then the default = 1)
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131
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132 - **classLabel** - a string indicating the experiment classes the samples belong to (e.g. control, QC, blank/placebo, exposed/treatment)
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133
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134 - **injectionOrder** - a numeric value indicating the order in which samples were analysed.
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135
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136 |
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137
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138 **ppm error tolerance** (REQUIRED; default = 2.0) - a numeric value equal-to or greater-than 0.
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139
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140 This parameter will influence the alignment of peaks from input peaklists. Peaks from distinct peaklists (corresponding to individual study samples) are aligned if the difference between their mass-to-charge ratios, when divided by the average of their mass-to-charge ratios and multiplied by 1 × 10\ :sup:`6` \, is equal-to or less-than than this parameter value (i.e. the difference between the mass-to-charge ratios, measured on the ppm scale, is less than the user-defined “ppm error tolerance”).
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141
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142 |
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143
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144 @help_options_addtional_output@
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145
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146 |
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147
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148 ------------------------------
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149
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150 Output file(s)
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151 --------------
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152
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153 @help_outputs_matrix@
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154
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155 -------------------------------------------------------------
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156
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157 @github_developers_contributors@
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158 @license@
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159 </help>
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160 <expand macro="citations" />
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161 </tool>