annotate extract_data_for_profrep.xml @ 6:1c25246f6e68 draft default tip

Uploaded
author petr-novak
date Thu, 27 Jun 2019 09:51:41 -0400
parents a5f1638b73be
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
1 <tool id="extract_data" name="Extract Data For ProfRep" version="1.0.0">
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
2 <requirements><requirement type="package" version="1.0.0">profrep</requirement></requirements>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
3 <description> Extract data for ProfRep from RepaetExplorer </description>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
4 <command>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
5 python3 ${__tool_directory__}/extract_data_for_profrep.py --re_archive ${re_archive} --output_cls ${output_cls} --output_reads_all ${output_reads_all} --output_annotation ${output_annotation}
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
6 </command>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
7 <inputs>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
8 <param format="zip" type="data" name="re_archive" label="RepeatExplorer output data archive" help="" />
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
9 </inputs>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
10
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
11 <outputs>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
12 <data format="fasta" name="output_cls" label="Output cls file of all clusters from ${re_archive.hid} archive" />
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
13 <data format="fasta" name="output_reads_all" label="Output file of all reads sequences from ${re_archive.hid} archive" />
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
14 <data format="tabular" name="output_annotation" label="Output file of clusters annotation from ${re_archive.hid} archive" />
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
15 </outputs>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
16
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
17 <help>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
18
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
19 **WHAT IT DOES**
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
20
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
21 This tool will extract all the necessary input data that are needed for ProfRep from RE output archive.
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
22 Use if the species is not already provided in our internal database (ProfRep drop-down menu -> Choose existing annotation dataset)
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
23
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
24
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
25 </help>
a5f1638b73be Uploaded
petr-novak
parents:
diff changeset
26 </tool>