Mercurial > repos > iuc > gff_to_prot

annotate convert_gff.xml @ 4:2aea122fbd25 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200"
author iuc
date Fri, 31 Jan 2020 10:49:13 -0500
parents 99810cf51f2e
children 79261884facd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
4
2aea122fbd25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200"
iuc
parents: 0
diff changeset
2 <tool id="gff_to_prot" name="Convert GFF3" version="@VERSION@+galaxy0">
0
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
3 <description>to prot_table for TRANSIT</description>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
4 <macros>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
5 <import>macros.xml</import>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
6 </macros>
4
2aea122fbd25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200"
iuc
parents: 0
diff changeset
7 <expand macro="requirements" />
2aea122fbd25 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 3a3bb179f4f3c99b25ef082996720c62aedb6200"
iuc
parents: 0
diff changeset
8 <command detect_errors="exit_code">transit convert gff_to_prot_table '$input' '$output'</command>
0
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
9 <inputs>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
10 <param name="input" type="data" format="gff3" label="GenBank GFF file" />
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
11 </inputs>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
12 <outputs>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
13 <data name="output" format="tabular" />
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
14 </outputs>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
15 <tests>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
16 <test>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
17 <param name="input" ftype="gff3" value="gff_to_prot-in1.gff3" />
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
18 <output name="output" file="gff_to_prot-out1.txt" />
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
19 </test>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
20 </tests>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
21
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
22 <help>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
23 <![CDATA[
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
24 .. class:: infomark
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
25
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
26
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
27 **What it does**
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
28
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
29 -------------------
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
30
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
31 Convert Gff3 files coming from Genbank in prot_table file that can be used as an input for TRANSIT tools.
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
32
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
33 ]]></help>
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
34 <expand macro="citations" />
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
35
99810cf51f2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents:
diff changeset
36 </tool>