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annotate topn.xml @ 11:14ccc766950f draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author tomnl
date Thu, 21 Jun 2018 08:45:42 -0400
parents 7353968f4980
children
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7353968f4980 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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1 <tool id="topn" name="topn" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" >r</requirement>
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4 <requirement type="package" >r-optparse</requirement>
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5 <requirement type="package" >r-xcmswrapper</requirement>
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6 </requirements>
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7 <description>Get the top (n) peaks in selected retention time windows of an LC-MS experiment
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8 </description>
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9
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13
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14 <command interpreter="Rscript"><![CDATA[
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15 topn.R
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16 --sample_metadata=$sample_metadata
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17 --out_dir=.
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18 --cores=\${GALAXY_SLOTS:-4}
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19 --galaxy_files='
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20 #for $i in $input
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21 $i,
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22 #end for
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23 '
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24 --files='
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25 #for $i in $input
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26 $i.name,
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27 #end for
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28 '
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29 #if $time_windows_cond.time_windows_choice== 'choose'
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30 --time_window_choice='
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31 #for $i, $j in enumerate($time_windows_cond.time_windows)
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32 $j.min,$j.max;
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33 #end for
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34 '
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35 #else
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36 --time_window_choice='0,90;90,660;660,1230;1230,1800;'
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37 #end if
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38 --file_include=$file_include
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39 --scan_dens=$scan_dens
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40 --n=$n
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41 --snthr=$snthr
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42 --minfrac=$minfrac
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43 --polarity=$polarity
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44 --class=$class
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45 --ppm=$ppm
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46
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47 ]]></command>
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48 <inputs>
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49
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50 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
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51 label="File(s) from your history containing your chromatograms"
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52 help="Select the dataset collection containing the files that were used
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53 for processing" />
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54
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55 <param name="sample_metadata" type="data" format="tsv, tabular"
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56 label="Sample meta-data"
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57 help="Metadata for each file (can re-use the sample meta-data file used for XCMS merge" />
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58
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59 <param name="class" type="text" label="class" value="blank"
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60 help="XCMS class to use (default is to use the blank)"/>
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61
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62 <param name="file_include" type="text" label="File include" value="2"
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63 help="Indexes of selected class to calculate topn on (comma separated string) e.g. 1,2"/>
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64
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65 <conditional name="time_windows_cond">
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66 <param name="time_windows_choice" type="select" label="time-windows"
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67 help="Default time-windows for 30 min (1800 secs) divided as follows (secs)- 0 : 90 : 660 : 1230 : 1800" >
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68 <option value="default_18000" selected="true">Default windows for 30 min run </option>
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69 <option value="choose">User defined windows</option>
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70 </param>
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71 <when value="choose">
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72 <repeat name="time_windows" title="Time windows">
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73 <param name="min" type="integer" label="min (sec)" value="0"/>
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74 <param name="max" type="integer" label="max (sec)" value="90"/>
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75 </repeat>
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76 </when>
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77 </conditional>
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78
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79 <param name="scan_dens" type="integer" label="Scan density" value="5"
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80 help="for scan range x to y, take every 'n' scan (i.e. x, x+n, x+2n ... y)"/>
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81
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82 <param name="n" type="integer" label="Number of peaks to select" value="100"
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83 help="The number of most intense peaks to select "/>
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84
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85 <param name="ppm" type="float" label="PPM tolerance" value="5"
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86 help="Parts per million tolerance for m/z between scans "/>
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87
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88 <param name="snthr" type="float" label="SNR threshold" value="100"
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89 help="Signal to noise threshold"/>
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90
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91 <param name="minfrac" type="float" label="minfrac" value="0.1" min="0" max="1"
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92 help="Minimum fraction peak has to be present in windows (typically set low to catch more peaks)"/>
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93 <param name="polarity" type="select" label="Polarity">
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94 <option value="positive" selected="true" >Positive</option>
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95 <option value="negative" >Negative</option>
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96 </param>
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97
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98
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99 </inputs>
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100 <outputs>
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101 <data name="topn_peaklist" format="tsv" label="topn_peaklist"
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102 from_work_dir="topn_peaklist.tsv" visible="true"/>
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103 </outputs>
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104 <tests>
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105 </tests>
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106 <help><![CDATA[
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107
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108 ]]></help>
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109 </tool>