Mercurial > repos > rjmw > dimspy_align_samples

annotate align_samples.xml @ 1:a941ec0fd2a4 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
author rjmw
date Wed, 30 May 2018 09:16:29 -0400
parents 50a090761d51
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50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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1 <tool id="dimspy_align_samples" name="Align Samples" version="1.0.0">
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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2 <description> - Align peaks across Peaklists</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 dimspy align-samples
1
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10 --input '$hdf5_file_in'
a941ec0fd2a4 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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11 --output '$hdf5_file_out'
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12 #if $filelist
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a941ec0fd2a4 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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13 --filelist '$filelist'
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14 #end if
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15 --ppm $ppm
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16 #if $hdf5_to_txt.standard
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17 &&
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18 @HDF5_PM_TO_TXT@
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19 #end if
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20 #if $hdf5_to_txt.comprehensive
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21 &&
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22 @HDF5_PM_TO_TXT_COMPREHENSIVE@
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23 #end if
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="" argument="--input"/>
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28 <param name="filelist" type="data" optional="true" format="tsv,tabular" 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." argument="--filelist"/>
a941ec0fd2a4 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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29 <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/>
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30 <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
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31 <expand macro="hdf5_pm_to_txt" />
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32 </inputs>
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33 <outputs>
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34 <expand macro="outputs_peak_intensity_matrix" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
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39 <param name="ppm" value="2.0"/>
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40 <param name="delimiter" value="tab"/>
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41 <param name="hdf5_to_txt|standard" value="True"/>
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42 <param name="hdf5_to_txt|comprehensive" value="False"/>
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43 <param name="hdf5_to_txt|samples_representations" value="rows"/>
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44 <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
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45 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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46 <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv" compare="sim_size"/>
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47 </test>
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48 <test>
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49 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
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50 <param name="ppm" value="2.0"/>
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51 <param name="delimiter" value="tab"/>
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52 <param name="hdf5_to_txt|standard" value="True"/>
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53 <param name="hdf5_to_txt|comprehensive" value="False"/>
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54 <param name="hdf5_to_txt|representation_samples" value="columns"/>
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55 <param name="hdf5_to_txt|matrix_attr" value="intensity"/>
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56 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
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57 <output name="matrix_file_out" file="peak_matrix_as_t.txt" ftype="tsv" compare="sim_size"/>
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58 </test>
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59 <test>
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60 <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
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61 <param name="ppm" value="2.0"/>
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62 <param name="delimiter" value="tab"/>
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63 <param name="hdf5_to_txt|standard" value="True"/>
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64 <param name="hdf5_to_txt|comprehensive" value="True"/>
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65 <param name="hdf5_to_txt|samples_representations" value="rows"/>
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66 <param name="hdf5_to_txt|matrix_attr" value="mz"/>
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67 <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
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68 <output name="matrix_file_out" file="peak_matrix_as_mz.txt" ftype="tsv" compare="sim_size"/>
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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69 <output name="matrix_comprehensive_file_out" file="peak_matrix_as_mz_compr.txt" ftype="tsv" compare="sim_size"/>
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70 </test>
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71 </tests>
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72 <help>
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73 -------------
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74 Align Samples
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75 -------------
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76
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77 Description
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78 -----------
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79
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80 | Use this tool to align Peaklists according to their constituent mass spectral peaks.
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81 | In the DIMS analysis workflow, align samples typically follows 'Replicate Filter'.
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82 | This tool may, however, be used to align any Peaklists (e.g. aligning individual Peaklists for each replicate of a sample).
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83
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84 Parameters
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85 ----------
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86
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87 **\1. Set of Peaklists (HDF5 file)** (REQUIRED)
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88
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89 For the default DIMS analysis workflow, this comprises a set of Peaklists output from the sequential application of the 'process_scans' tools, followed by the 'replicate_filter' tool.
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92 **\2. Filelist / Samplelist** (OPTIONAL)
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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93
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94 | A tabular-formatted .txt file with columns: filename, batch, classLabel, injectionOrder.
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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95 | Additional collumns are allowed but are not used during processing.
50a090761d51 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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96 | This file must be uploaded in to (or available from) the current history in order to allow for it to be selected from the drop-down menu.
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a941ec0fd2a4 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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97 | **NOTE:** Only provide a filelist if you like to exclude Peaklist, update the metadata (e.g. classLabel), or if you have not provided a filelist for 'Process Scans' or Replicate Filter'.
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98 |
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99
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100 <![CDATA[
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101
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102 +-------------------------------+-------+------------+----------------+
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103 | filename | batch | classLabel | injectionOrder |
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104 +-------------------------------+-------+------------+----------------+
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105 | sample_rep1_rep3_rep4 | 1 | sample | 1 |
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106 +-------------------------------+-------+------------+----------------+
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107 | blank_rep1_rep2_rep3 | 1 | sample | 2 |
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108 +-------------------------------+-------+------------+----------------+
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109 | ... | ... | ... | ... |
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110 +-------------------------------+-------+------------+----------------+
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111
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112 ]]>
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114 **\3. ppm** (REQUIRED; default = 2.0)
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115
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116 | A numeric value from 0 upwards.
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117 | Peaks with m/z differences (measured in parts-per-million) below this value are clustered together as a single feature.
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118 |
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119
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120 @help_options_addtional_output@
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121
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122 @github_developers_contributors@
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123
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124 </help>
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125 <expand macro="citations" />
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126 </tool>