Mercurial > repos > mheinzl > hd
comparison hd.xml @ 22:7e570ba56b83 draft
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 |
comparison
equal
deleted
inserted
replaced
| 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 |