Mercurial > repos > iuc > colibread_mapsembler2

comparison mapsembler2.xml @ 6:e8a8cb93878a 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/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:52:52 +0000
parents 71d60a931e2f
children
comparison
equal deleted inserted replaced
5:71d60a931e2f 6:e8a8cb93878a
1 <tool id="mapsembler2" name="Mapsembler2" version="2.2.4+galaxy0" profile="@PROFILE@"> 1 <tool id="mapsembler2" name="Mapsembler2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>is a targeted assembly software</description> 2 <description>is a targeted assembly software</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.2.4</token>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="2.2.4">mapsembler2</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">mapsembler2</requirement>
8 </requirements> 9 </requirements>
9 <command><![CDATA[ 10 <command><![CDATA[
10 #import re 11 #import re
11 #set $starter_filename = re.sub('[^\w_]', '_', $s.element_identifier) + ".fasta" 12 #set $starter_filename = re.sub('[^\w_]', '_', $s.element_identifier) + ".fasta"
12 #if $s.ext.endswith('.gz'): 13 #if $s.ext.endswith('.gz'):
50 </param> 51 </param>
51 <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/> 52 <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/>
52 <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/> 53 <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
53 </inputs> 54 </inputs>
54 <outputs> 55 <outputs>
55 <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/> 56 <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Assembly"/>
56 <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="Coherent with ${tool.name} on $on_string" hidden="true"/> 57 <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Coherent" hidden="true"/>
57 <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="Uncoherent with ${tool.name} on $on_string" hidden="true"/> 58 <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Uncoherent" hidden="true"/>
58 <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/> 59 <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="${tool.name} on ${on_string}: Starter extremities" hidden="true"/>
59 </outputs> 60 </outputs>
60 <tests> 61 <tests>
61 <test> 62 <test>
62 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/> 63 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
63 <param name="r" value="mapsembler2/reads1.gz,mapsembler2/reads2.gz" ftype="fasta.gz"/> 64 <param name="r" value="mapsembler2/reads1.gz,mapsembler2/reads2.gz" ftype="fasta.gz"/>