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comparison hd.xml @ 22:7e570ba56b83 draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
author mheinzl
date Wed, 27 Feb 2019 04:50:56 -0500
parents b084b6a8e3ac
children ffd105ac12fb
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21:9919024d7778 22:7e570ba56b83
5 <requirement type="package" version="2.7">python</requirement> 5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package" version="1.4.0">matplotlib</requirement> 6 <requirement type="package" version="1.4.0">matplotlib</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 python2 '$__tool_directory__/hd.py' --inputFile '$inputFile' --inputName1 '$inputFile.name' --sample_size $sampleSize --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS 9 python2 '$__tool_directory__/hd.py' --inputFile '$inputFile' --inputName1 '$inputFile.name' --sample_size $sampleSize --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS
10 $nr_above_bars --output_pdf $output_pdf --output_tabular $output_tabular 10 $nr_above_bars --output_pdf $output_pdf --output_tabular $output_tabular --output_chimeras_tabular $output_chimeras_tabular
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="inputFile" type="data" format="tabular" label="Dataset 1: input tags" optional="false" help="Input in tabular format with the family size, tag and the direction of the strand ('ab' or 'ba') for each family."/> 13 <param name="inputFile" type="data" format="tabular" label="Dataset 1: input tags" optional="false" help="Input in tabular format with the family size, tag and the direction of the strand ('ab' or 'ba') for each family."/>
14 <param name="sampleSize" type="integer" label="number of tags in the sample" value="1000" min="0" help="specifies the number of tags in one analysis. If sample size is 0, all tags of the dataset are compared against all tags."/> 14 <param name="sampleSize" type="integer" label="number of tags in the sample" value="1000" min="0" help="specifies the number of tags in one analysis. If sample size is 0, all tags of the dataset are compared against all tags."/>
15 <param name="minFS" type="integer" label="minimum family size of the tags" min="1" value="1" help="filters the tags after their family size: Families with a smaller size are skipped. Default: min. family size = 1."/> 15 <param name="minFS" type="integer" label="minimum family size of the tags" min="1" value="1" help="filters the tags after their family size: Families with a smaller size are skipped. Default: min. family size = 1."/>
19 <param name="nproc" type="integer" label="number of processors" value="8" help="Number of processor used for computing."/> 19 <param name="nproc" type="integer" label="number of processors" value="8" help="Number of processor used for computing."/>
20 <param name="nr_above_bars" type="boolean" label="include numbers above bars?" truevalue="--nr_above_bars" falsevalue="" checked="True" help="The absolute and relative values of the data can be included or removed from the plots. "/> 20 <param name="nr_above_bars" type="boolean" label="include numbers above bars?" truevalue="--nr_above_bars" falsevalue="" checked="True" help="The absolute and relative values of the data can be included or removed from the plots. "/>
21 21
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <data name="output_pdf" format="pdf" />
24 <data name="output_tabular" format="tabular"/> 25 <data name="output_tabular" format="tabular"/>
25 <data name="output_pdf" format="pdf" /> 26 <data name="output_chimeras_tabular" format="tabular"/>
27
26 </outputs> 28 </outputs>
27 <tests> 29 <tests>
28 <test> 30 <test>
29 <param name="inputFile" value="Test_data.tabular"/> 31 <param name="inputFile" value="Test_data.tabular"/>
30 <param name="sampleSize" value="0"/> 32 <param name="sampleSize" value="0"/>
31 <output name="output_pdf" file="output_file.pdf" lines_diff="6"/> 33 <output name="output_pdf" file="output_file.pdf" lines_diff="6"/>
32 <output name="output_tabular" file="output_file.tabular"/> 34 <output name="output_tabular" file="output_file.tabular"/>
35 <output name="output_chimeras_tabular" file="output_file_chimeras.tabular"/>
33 </test> 36 </test>
34 </tests> 37 </tests>
35 <help> <![CDATA[ 38 <help> <![CDATA[
36 **What it does** 39 **What it does**
37 40
78 these data can now be used in this tool. 81 these data can now be used in this tool.
79 82
80 83
81 **Output** 84 **Output**
82 85
83 The output is one PDF file with the plots of the Hamming distance and a tabular file with the data of the plot for each dataset. 86 The output is one PDF file with the plots of the Hamming distance, a tabular file with the data of the plot for each dataset and a tabular file with tags that are chimeric.
84 87
85 88
86 **About Author** 89 **About Author**
87 90
88 Author: Monika Heinzl 91 Author: Monika Heinzl