Mercurial > repos > erasmus-medical-center > gfa_to_fa

annotate gfa_to_fa.xml @ 0:a9447e4a5634 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
author erasmus-medical-center
date Tue, 17 Jul 2018 10:31:08 -0400
parents
children 810d464f9359
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
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1 <tool id="gfa_to_fa" name="GFA to Fasta" version="0.1.0">
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
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2 <description>Convert GFA files to Fasta </description>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
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3 <command detect_errors="exit_code"><![CDATA[
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
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4 cat $in_gfa | python $convert > '$out_fa'
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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5 ]]>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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6 </command>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
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7 <configfiles>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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8 <configfile name="convert"><![CDATA[
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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9 from __future__ import print_function
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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10 import sys
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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11 for line in sys.stdin:
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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12 if line.startswith("S"):
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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13 l,h,s,x = line.strip().split()
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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14 print("> " + h)
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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15 print(s)
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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16 ]]>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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17 </configfile>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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18 </configfiles>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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19 <inputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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20 <param name="in_gfa" type="data" format="tabular" label="Input GFA file" />
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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21 </inputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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22 <outputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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23 <data name="out_fa" format="fasta" label="${tool.name} on ${on_string}: Fasta file" />
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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24 </outputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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25 <tests>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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26 <test>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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27 <param name="in_gfa" value="test.gfa"/>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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28 <output name="out_fa" file="out.fa"/>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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29 </test>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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30 </tests>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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31 <help><![CDATA[
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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32 gfa_to_fa converts a GFA file to a Fasta File. The column two from the GFA file is used as sequence header.
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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33 ]]></help>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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34 </tool>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
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