Mercurial > repos > rjmw > dimspy_process_scans

annotate macros.xml @ 0:d129e75a31d9 draft

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planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
author rjmw
date Tue, 27 Feb 2018 14:04:01 -0500
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0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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1 <macros>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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2 <xml name="requirements">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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3 <requirements>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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4 <requirement type="package" version="1.1.0">dimspy</requirement>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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5 </requirements>
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6 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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7 <xml name="stdio">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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8 <stdio>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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9 <exit_code range="1:" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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10 </stdio>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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11 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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12
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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13 <token name="@HDF5_PM_TO_TXT@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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14 dimspy hdf5-pm-to-txt
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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15 --input "$hdf5_file_out"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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16 --output "$matrix_file_out"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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17 --delimiter $delimiter
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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18 --attribute_name $hdf5_to_txt.matrix_attr
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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19 --representation-samples $hdf5_to_txt.representation_samples
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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20 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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21
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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22 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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23 dimspy hdf5-pm-to-txt
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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24 --input "$hdf5_file_out"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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25 --output "$matrix_comprehensive_file_out"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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26 --delimiter $delimiter
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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27 --comprehensive
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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28 --attribute_name $hdf5_to_txt.matrix_attr
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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29 --representation-samples $hdf5_to_txt.representation_samples
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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30 </token>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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31
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32 <xml name="hdf5_pm_to_txt">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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33 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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34 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to &quot;yes&quot; to produce a &quot;standard&quot; Peak Matrix (i.e. m/z and intensity)."/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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35 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to &quot;yes&quot; to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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36 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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37 <option value="rows" selected="true">Rows</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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38 <option value="columns">Columns</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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39 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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40 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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41 <option value="intensity" selected="true">Intensity</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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42 <option value="mz">m/z</option>
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43 <option value="snr">Signal-to-noise ratio (SNR)</option>
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44 </param>
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45 </section>
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46 </xml>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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47
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48 <xml name="outputs_peak_intensity_matrix">
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49 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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50 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
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51 <filter>hdf5_to_txt["standard"] is True</filter>
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52 </data>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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53 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
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54 <filter>hdf5_to_txt["comprehensive"] is True</filter>
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55 </data>
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56 </xml>
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57
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58 <xml name="citations">
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59 <citations>
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60 <citation type="doi">10.1038/nprot.2016.156</citation>
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61 <citation type="doi">10.1038/sdata.2014.12</citation>
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62 <citation type="doi">10.1021/ac062446p</citation>
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63 <citation type="doi">10.1021/ac2001803</citation>
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64 <yield />
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65 </citations>
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66 </xml>
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67
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68 <token name="@example_filelist@">
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69 <![CDATA[
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70
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71 +-----------------+-----------+-------+------------+----------------+
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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72 | filename | replicate | batch | classLabel | injectionOrder |
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73 +-----------------+-----------+-------+------------+----------------+
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74 | sample_rep1.raw | 1 | 1 | sample | 1 |
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75 +-----------------+-----------+-------+------------+----------------+
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76 | sample_rep2.raw | 2 | 1 | sample | 2 |
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77 +-----------------+-----------+-------+------------+----------------+
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78 | sample_rep3.raw | 3 | 1 | sample | 3 |
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79 +-----------------+-----------+-------+------------+----------------+
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80 | sample_rep4.raw | 4 | 1 | sample | 4 |
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81 +-----------------+-----------+-------+------------+----------------+
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82 | blank_rep1.raw | 1 | 1 | blank | 5 |
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83 +-----------------+-----------+-------+------------+----------------+
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84 | blank_rep2.raw | 2 | 1 | blank | 6 |
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85 +-----------------+-----------+-------+------------+----------------+
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86 | blank_rep3.raw | 3 | 1 | blank | 7 |
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87 +-----------------+-----------+-------+------------+----------------+
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88 | blank_rep4.raw | 4 | 1 | blank | 8 |
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89 +-----------------+-----------+-------+------------+----------------+
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90 | ... | ... | ... | ... | ... |
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91 +-----------------+-----------+-------+------------+----------------+
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92
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93 ]]>
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94 </token>
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95
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96
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97 <token name="@help_options_addtional_output@">
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98 |
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99 | **Show options for additonal output(s)** (OPTIONAL)
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100 |
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101
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102 **\A. Standard output** (default = &quot;No&quot;)
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103
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104 Boolean toggle where selection of:
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105
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106 - &quot;Yes&quot; will generate a .txt formatted Peak Matrix (i.e. m/z and intensity).
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107 - &quot;No&quot; will prevent the creation of a .txt formatted Peak Matrix.
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108
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109 **\B. Comprehensive output** (default = &quot;No&quot;)
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110
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111 Boolean toggle where selection of:
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112
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113 - &quot;Yes&quot; generates a Peak Matrix containing the m/z, intensity, missing values and other metrics associated with the aligned peaks.
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114 - &quot;No&quot; will prevent the creation of a .txt formatted comprehensive Peak Matrix..
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115
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116 **\C. Should rows or columns represent the samples?** (default = &quot;rows&quot;)
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117
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118 Binary toggle (default = &quot;rows&quot;) where selection of:
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119
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120 - &quot;rows&quot; puts sample information in to the rows and m/z values (for aligned mass spectral peaks) in to columns of any output Peak Matrix.
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121 - &quot;columns&quot; puts sample information in the columns and m/z values (for aligned mass spectral peaks) in to the rows of any output Peak Matrix.
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122
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123 **\D. The Peak Matrix should contain ... values**
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124
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125 Use this option to define which metric is inserted in to the cells of the output Peak Matrix.
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126
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127 - &quot;Intensity&quot; writes the absolute peak intensity to the Peak Matrix.
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128 - &quot;m/z&quot; writes the m/z value to the Peak Matrix.
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129 - &quot;Signal-to-noise ratio (SNR)&quot; writes the signal-to-noise ratio to the Peak Matrix.
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130
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131 Output file(s)
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132 --------------
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133
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134 | A HDF5 file containing a Peak Matrix
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135 |
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136 | **OPTIONAL**
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137 | A (standard and/or comprehenstive) Peak Matrix comprising samples on one axis and m/z values on the perpendicular axis
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138 |
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139
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140 - Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
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141 - File only created if user toggles &quot;Standard output&quot; and/or &quot;Comprehensive output&quot; to &quot;Yes&quot;
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142 - By default, samples are in rows and peaks are in columns. Altering the &quot;Should rows or columns represent samples&quot; toggle will transpose this matrix.
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143
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144 </token>
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145
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146 <token name="@github_developers_contributors@">
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147 Github respository (source code)
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148 --------------------------------
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149
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150 https://github.com/computational-metabolomics/dimspy-galaxy/
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151
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152 Developers and contributors
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153 ---------------------------
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154
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155 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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156 - **Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)**
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157 - **Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)**
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158
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159 |
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160 </token>
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161
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162 </macros>