Mercurial > repos > mheinzl > fsd
changeset 6:c4b8222dce29 draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 1667d50b521325eea1eada1b16029b1ba1379c5f
| author | mheinzl |
|---|---|
| date | Wed, 09 May 2018 09:20:06 -0400 |
| parents | 69f47e0b804e |
| children | 43b16247c35a |
| files | fsd.py fsd.xml |
| diffstat | 2 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/fsd.py Wed May 09 09:13:46 2018 -0400 +++ b/fsd.py Wed May 09 09:20:06 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('--inputFile1', + 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.') @@ -53,9 +53,9 @@ parser = make_argparser() args=parser.parse_args(argv[1:]) - #firstFile = args.inputFile + firstFile = args.inputFile1 name1 = args.inputName1 - firstFile = args.inputName1 + #firstFile = args.inputName1 secondFile = args.inputFile2 name2 = args.inputName2
--- a/fsd.xml Wed May 09 09:13:46 2018 -0400 +++ b/fsd.xml Wed May 09 09:20:06 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="0.0.6"> +<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.7"> <description>Family size distribution (FSD) of tags</description> <requirements> <requirement type="package" version="1.4">matplotlib</requirement> </requirements> <command> - 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 + python $__tool_directory__/fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_csv $output_csv --output_pdf $output_pdf </command> <inputs> <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>