Mercurial > repos > mheinzl > fsd
changeset 5:69f47e0b804e draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 9829d657c07703b117bed2f259ddba432b244312
| author | mheinzl |
|---|---|
| date | Wed, 09 May 2018 09:13:46 -0400 |
| parents | 5bae51dc7fa1 |
| children | c4b8222dce29 |
| files | fsd.py fsd.xml |
| diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/fsd.py Wed May 09 09:09:26 2018 -0400 +++ b/fsd.py Wed May 09 09:13:46 2018 -0400 @@ -29,8 +29,8 @@ def make_argparser(): parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data') - parser.add_argument('inputFile', - help='Tabular File with three columns: ab or ba, tag and family size.') + # parser.add_argument('inputFile', + # help='Tabular File with three columns: ab or ba, tag and family size.') parser.add_argument('--inputName1') parser.add_argument('--inputFile2',default=None, help='Tabular File with three columns: ab or ba, tag and family size.') @@ -53,8 +53,10 @@ parser = make_argparser() args=parser.parse_args(argv[1:]) - firstFile = args.inputFile + #firstFile = args.inputFile name1 = args.inputName1 + firstFile = args.inputName1 + secondFile = args.inputFile2 name2 = args.inputName2 thirdFile = args.inputFile3
--- a/fsd.xml Wed May 09 09:09:26 2018 -0400 +++ b/fsd.xml Wed May 09 09:13:46 2018 -0400 @@ -1,13 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!-- galaxy version 16.04 --> -<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.5"> +<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.6"> <description>Family size distribution (FSD) of tags</description> <requirements> <requirement type="package" version="1.4">matplotlib</requirement> </requirements> <command> - python $__tool_directory__/fsd.py $file1.name --inputName1 $file1.name --inputFile2 $file2.name --inputName2 $file2.name --inputFile3 $file3.name --inputName3 $file3.name --inputFile4 $file4.name --inputName4 $file4.name --sep $separator --output_csv $output_csv --output_pdf $output_pdf + python $__tool_directory__/fsd.py --inputName1 $file1.name --inputFile2 $file2.name --inputName2 $file2.name --inputFile3 $file3.name --inputName3 $file3.name --inputFile4 $file4.name --inputName4 $file4.name --sep $separator --output_csv $output_csv --output_pdf $output_pdf </command> <inputs> <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>