Mercurial > repos > erasmus-medical-center > gfa_to_fa

annotate gfa_to_fa.xml @ 2:a54fa2c9503f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit a00033a6cd8deb6b4a35ec1f4adb20dcc83cd1a1
author erasmus-medical-center
date Fri, 20 Jul 2018 08:19:46 -0400
parents 810d464f9359
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
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
parents:
diff changeset
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
parents:
diff changeset
3 <command detect_errors="exit_code"><![CDATA[
1
810d464f9359 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 1a253e02d30317fb231294b55291df79b1cda568
erasmus-medical-center
parents: 0
diff changeset
4 cat '$in_gfa' | python $convert > '$out_fa'
810d464f9359 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 1a253e02d30317fb231294b55291df79b1cda568
erasmus-medical-center
parents: 0
diff changeset
5 ]]></command>
0
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
6 <configfiles>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
7 <configfile name="convert"><![CDATA[
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
8 from __future__ import print_function
1
810d464f9359 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 1a253e02d30317fb231294b55291df79b1cda568
erasmus-medical-center
parents: 0
diff changeset
9 import sys
0
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
10 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
erasmus-medical-center
parents:
diff changeset
11 if line.startswith("S"):
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
12 l,h,s,x = line.strip().split()
2
a54fa2c9503f planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit a00033a6cd8deb6b4a35ec1f4adb20dcc83cd1a1
erasmus-medical-center
parents: 1
diff changeset
13 print(">" + h)
0
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
14 print(s)
1
810d464f9359 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 1a253e02d30317fb231294b55291df79b1cda568
erasmus-medical-center
parents: 0
diff changeset
15 ]]></configfile>
0
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
16 </configfiles>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
17 <inputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
18 <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
erasmus-medical-center
parents:
diff changeset
19 </inputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
20 <outputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
21 <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
erasmus-medical-center
parents:
diff changeset
22 </outputs>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
23 <tests>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
24 <test>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
25 <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
erasmus-medical-center
parents:
diff changeset
26 <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
erasmus-medical-center
parents:
diff changeset
27 </test>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
28 </tests>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
29 <help><![CDATA[
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
30 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
erasmus-medical-center
parents:
diff changeset
31 ]]></help>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
32 </tool>
a9447e4a5634 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/gfa_to_fa commit 5d58728b8831bcdd98b8162e6163035bfd00d0d6
erasmus-medical-center
parents:
diff changeset
33