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comparison fsd_beforevsafter.xml @ 1:6ed6dca9488f draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_beforevsafter commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
author mheinzl
date Sat, 12 May 2018 04:51:34 -0400
parents 6716b1cddf3e
children e8115b71edbd
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0:6716b1cddf3e 1:6ed6dca9488f
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="fsd_beforevsafter" name="Duplex Sequencing Analysis:" version="0.0.1"> 2 <tool id="fsd_beforevsafter" name="Duplex Sequencing Analysis:" version="0.0.2">
3 <requirements> 3 <requirements>
4 <!-- galaxy version 16.04 --> 4 <!-- galaxy version 16.04 -->
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">matplotlib</requirement> 6 <requirement type="package" version="1.4">matplotlib</requirement>
7 <requirement type="package" version="1.70">biopython</requirement> 7 <requirement type="package" version="1.7">biopython</requirement>
8 8
9 </requirements> 9 </requirements>
10 <description>Family size distribution (FSD) of tags from various steps of the Du Novo pipeline</description> 10 <description>Family size distribution (FSD) of tags from various steps of the Du Novo pipeline</description>
11 <command> 11 <command>
12 python2 $__tool_directory__/fsd_beforevsafter.py --inputFile_SSCS "$file1" --makeDCS "$makeDCS" --afterTrimming "$afterTrimming" --alignedTags "$alignedTags" --sep $separator --output_csv $output_csv --output_pdf $output_pdf 12 python2 $__tool_directory__/fsd_beforevsafter.py --inputFile_SSCS "$file1" --makeDCS "$makeDCS" --afterTrimming "$afterTrimming" --alignedTags "$alignedTags" --sep $separator --output_csv $output_csv --output_pdf $output_pdf
40 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab | 40 | 28 | AAAAAAAAAAATGGTATGGACCGA | ab |
41 +-----+----------------------------+----+ 41 +-----+----------------------------+----+
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45 **Dataset 2:** And a fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by Du Novo: make families. 45 **Dataset 2:** And a fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by Du Novo: make consensus reads.
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48 **Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given. 48 **Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given.
49 For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool. 49 For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool.
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