Mercurial > repos > mheinzl > fsd
diff fsd.xml @ 16:6bd9ef49d013 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
| author | mheinzl |
|---|---|
| date | Mon, 08 Oct 2018 05:50:18 -0400 |
| parents | 32921a67437b |
| children | 2e517a54eedc |
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--- a/fsd.xml Tue Jul 17 07:09:21 2018 -0400 +++ b/fsd.xml Mon Oct 08 05:50:18 2018 -0400 @@ -1,80 +1,72 @@ <?xml version="1.0" encoding="UTF-8"?> <!-- galaxy version 16.04 --> -<tool id="fsd" name="Duplex Sequencing Analysis: fsd" version="0.0.16"> - <description>Family size distribution (FSD) of tags</description> +<tool id="fsd" name="FSD" version="1.0.0"> + <description>: Family Size Distribution of duplex sequencing tags</description> <requirements> <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.4">matplotlib</requirement> - <requirement type="package" version="0.0.2">duplexanalysis</requirement> - + <requirement type="package" version="1.4.0">matplotlib</requirement> </requirements> <command> - fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_pdf $output_pdf --output_csv $output_csv + python2 '$__tool_directory__/fsd.py' --inputFile1 '${file1}' --inputName1 '${file1.name}' +--inputFile2 '${file2}' --inputName2 '${file2.name}' --inputFile3 '${file3}' --inputName3 '${file3.name}' +--inputFile4 '${file4}' --inputName4 '${file4.name}' --output_pdf $output_pdf --output_tabular $output_tabular </command> <inputs> <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/> <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true" /> <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" /> <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters!"/> - <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/> </inputs> <outputs> <data name="output_pdf" format="pdf" /> - <data name="output_csv" format="csv"/> + <data name="output_tabular" format="tabular"/> </outputs> - <!-- <tests> + <tests> <test> <param name="file1" value="Test_data.tabular"/> - <param name="file2" value="None"/> - <param name="file3" value="None"/> - <param name="file4" value="None"/> - <output name="output_pdf" file="output_file.pdf"/> - <output name="output_csv" file="output_file.csv"/> + <param name="file2" value="Test_data2.tabular"/> + <param name="file3" value="Test_data3.tabular"/> + <param name="file4" value="Test_data4.tabular"/> + <output name="output_pdf" file="output_file.pdf" lines_diff="285"/> + <output name="output_tabular" file="output_file.tabular"/> + </test> + <test> + <param name="file1" value="Test_data.tabular"/> + <param name="file2" value="Test_data2.tabular"/> + <param name="file3" value="Test_data3.tabular"/> + <output name="output_pdf" file="output_file2.pdf" lines_diff="285"/> + <output name="output_tabular" file="output_file2.tabular"/> </test> </tests> - --> - <help> <![CDATA[ + <help><![CDATA[ **What it does** - This tool will create a distribution of family sizes of each tag, which is separated after families tags that have only the forward (ab) strand, the reverse (ba) strand or both strands (ab+ba) of the DCS and a family size distribution without separation is created. If multiple files are provided as input, the family size distribution without separation contains all datasets in one plot and for each dataset a distribution with separation after single ab, ba strands and DCSs is produced. - +This tool will create a distribution of family sizes of each tag, which is separated after tags that have only the forward (ab) strand, the reverse (ba) strand or both strands (ab+ba) of the DCS and a family size distribution without separation is created. + +------ **Input** - This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. - - **!!! Name of the files can have max. 34 charcters !!!** - - +-----+----------------------------+----+ - | 1 | AAAAAAAAAAAATGTTGGAATCTT | ba | - +-----+----------------------------+----+ - | 10 | AAAAAAAAAAAGGCGGTCCACCCC | ab | - +-----+----------------------------+----+ - | 28 | AAAAAAAAAAATGGTATGGACCGA | ab | - +-----+----------------------------+----+ - - - - - +This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands:: + + 1 AAAAAAAAAAAATGTTGGAATCTT ba + 10 AAAAAAAAAAAGGCGGTCCACCCC ab + 28 AAAAAAAAAAATGGTATGGACCGA ab + **Output** - The output is a PDF file with the plot and a CSV with the data of the plot. - +The output is a PDF file with the plot and a tabular file with the data of the plot. **About Author** - Author: Monika Heinzl - - Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria - - Contact: monika.heinzl@edumail.at +Author: Monika Heinzl +Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria +Contact: monika.heinzl@edumail.at - ]]> - - </help> +]]> +</help> <citations> <citation type="bibtex"> @misc{duplex,