Mercurial > repos > malex > secimtools

annotate magnitude_difference_flags.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
parents
children caba07f41453
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2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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1 <tool id="secimtools_magnitude_difference_flags" name="Magnitude Difference Flags" version="@WRAPPER_VERSION@">
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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2 <description>- Count the number of digits before the decimal place.</description>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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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" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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7 <command detect_errors="exit_code"><![CDATA[
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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8 magnitude_difference_flags.py
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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9 --input $input
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10 --design $design
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11 --ID $uniqID
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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12 --flags $flags
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13 --figure $figure
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14 --counts "counts"
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15 --html $html
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16 --htmlPath "$html.files_path"
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17
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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18 #if $nozero:
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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19 --noZero
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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20 #end if
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21 #if $group:
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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22 --group $group
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23 #end if
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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24 ]]></command>
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25 <inputs>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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26 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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27 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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28 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers.."/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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29 <param name="nozero" type="select" size="30" display="radio" value="yes" label="Remove zeros before processing" help="If not removed, zeros may skew the results.">
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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30 <option value="yes">Remove zeros</option>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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31 <option value="no">Do not remove zeros</option>
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32 </param>
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33 <param name="group" size="30" type="text" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classifications." />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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34 </inputs>
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35 <outputs>
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36 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: Figure" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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37 <data format="tabular" name="flags" label="C${tool.name} on ${on_string}: Flags" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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38 <data format="html" name="html" label="${tool.name} on ${on_string}: Counts" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="ST000006_data.tsv"/>
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43 <param name="design" value="ST000006_design.tsv"/>
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44 <param name="uniqID" value="Retention_Index" />
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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45 <param name="group" value="White_wine_type_and_source" />
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46 <param name="nonzero" value="yes" />
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47 <output name="figure" file="ST000006_magnitude_difference_flags_figure.pdf" compare="sim_size" delta="10000"/>
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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48 <output name="flags" file="ST000006_magnitude_difference_flags_flags.tsv" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52
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53 @TIP_AND_WARNING@
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54
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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55 **Tool Description**
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56
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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57 This tool counts the number of digits before the decimal place for each feature in each sample.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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58 The tool identifies features with different orders of magnitude across different samples in a given group and produces corresponding indicator flags.
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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59 Unusual samples are identified by finding systematically low or high feature values for that particular sample.
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60
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61 --------------------------------------------------------------------------------
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62
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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63 **Input**
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64
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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65 - Two input datasets are required.
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66
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67 @WIDE@
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68
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69 **NOTE:** The sample IDs must match the sample IDs in the Design File
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70 (below). Extra columns will automatically be ignored.
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71
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72 @METADATA@
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73
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74 @UNIQID@
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75
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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76 **Remove zeros before processing**
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77
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78 - If zeros are not removed before processing, they may skew the results.
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79
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80 @GROUP_OPTIONAL@
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81
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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82 **NOTE:** Groups with one element will be excluded from the test.
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83
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84 --------------------------------------------------------------------------------
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85
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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86 **Output**
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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87
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88 The tool outputs a variable number of files (from 2 to n+1) depending on the number of groups (n).
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89
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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90 (1) TSV file containing a 0/1 indicator flag where “1” is used to flag features where the difference in the digit counts is greater than 2.
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91
2e7d47c0b027 "planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
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92 (2) TSV file containing the digit counts for all samples or for the samples within groups, depending on whether the Group/Treatment [Optional] parameter was provided.
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93
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94 (3) A PDF file of the distribution of digit counts within each group of samples.
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95
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96 ]]></help>
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97 <expand macro="citations"/>
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98 </tool>