Mercurial > repos > iuc > gfa_to_fa

annotate gfa_to_fa.xml @ 2:43f7a0890015 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"
author iuc
date Wed, 03 Mar 2021 17:17:23 +0000
parents bb94cb83d936
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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43f7a0890015 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"
iuc
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1 <tool id="gfa_to_fa" name="GFA to FASTA" version="0.1.2">
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48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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2 <description>Convert Graphical Fragment Assembly files to FASTA format </description>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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3 <command detect_errors="exit_code"><![CDATA[
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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4 cat '$in_gfa' | python '$convert' > '$out_fa'
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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5 ]]></command>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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6 <configfiles>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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7 <configfile name="convert"><![CDATA[
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
iuc
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8 from __future__ import print_function
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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9 import sys
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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10 for line in sys.stdin:
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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11 if line.startswith("S"):
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43f7a0890015 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"
iuc
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12 l,h,s = line.strip().split('\t')[:3]
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bb94cb83d936 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 518c9f5ae1d6dfddd26bc37107e06f269147ed55"
iuc
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13 print(">" + h)
bb94cb83d936 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 518c9f5ae1d6dfddd26bc37107e06f269147ed55"
iuc
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14 print(s)
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48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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15 ]]></configfile>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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16 </configfiles>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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17 <inputs>
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43f7a0890015 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit 83aed19c6cdf00f3133eb80a69cba0074ca244cc"
iuc
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18 <param name="in_gfa" type="data" format="tabular,gfa1" label="Input GFA file" />
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48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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19 </inputs>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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20 <outputs>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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21 <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" />
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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22 </outputs>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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23 <tests>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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24 <test>
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25 <param name="in_gfa" value="test.gfa"/>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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26 <output name="out_fa" file="out.fa"/>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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27 </test>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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28 </tests>
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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29 <help><![CDATA[
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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30 This tool converts a GFA file (Graphical Fragment Assembly) to a FASTA file. The second column from the GFA file is used as the sequence header.
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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32 More information about the GFA file format can be found here_
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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34 .. _here: http://gfa-spec.github.io/GFA-spec/GFA1.html
48408c58c6e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa commit dfcdad14da6311657c8609074b95fdb56939bca1
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35 ]]></help>
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36 </tool>
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