Mercurial > repos > fangly > grinder

comparison tools/ngs_simulation/grinder.xml @ 2:27a15723d4f0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fangly
date Tue, 04 Oct 2011 01:02:12 -0400
parents 7d26d64539b2
children
comparison
equal deleted inserted replaced
1:7d26d64539b2 2:27a15723d4f0
1 <tool id="grinder" name="Grinder" version="0.3.7" force_history_refresh="True"> 1 <tool id="grinder" name="Grinder" version="0.3.8" force_history_refresh="True">
2 2
3 <!-- 3 <!--
4 Author: florent.angly@gmail.com 4 Author: florent.angly@gmail.com
5 TODO: 5 TODO:
6 • See bfast tool (tools/sr_mapping/bfast_wrapper.xml) for how to use datatables easily 6 • See bfast tool (tools/sr_mapping/bfast_wrapper.xml) for how to use datatables easily
7 • Basic tests 7 • Basic tests
8 • Link to full manual 8 • Link to full manual
9 • Better sync with Grinder parameters, defaults and help 9 • Better sync with Grinder parameters, defaults and help
10 --> 10 -->
11 11
12 <description>genomic, metagenomic and amplicon read simulator (BETA)</description> 12 <description>genomic, metagenomic and amplicon read simulator</description>
13 13
14 <requirements> 14 <requirements>
15 <requirement type="binary">grinder</requirement> 15 <requirement type="binary">grinder</requirement>
16 </requirements> 16 </requirements>
17 17
98 #if str($permuted_perc): 98 #if str($permuted_perc):
99 -desc_track $desc_track 99 -desc_track $desc_track
100 #end if 100 #end if
101 #if str($qual_levels): 101 #if str($qual_levels):
102 -qual_levels $qual_levels 102 -qual_levels $qual_levels
103 #end if
104 #if str($fastq_output):
105 -fastq_output $fastq_output
103 #end if 106 #end if
104 #if str($profile_file) != "None": 107 #if str($profile_file) != "None":
105 -profile_file $profile_file.value 108 -profile_file $profile_file.value
106 #end if 109 #end if
107 <!-- When Galaxy bug #661 is resolved, then we can use the same method to check for all optional argument --> 110 <!-- When Galaxy bug #661 is resolved, then we can use the same method to check for all optional argument -->
213 216
214 <param name="desc_track" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Read tracking" help="Track read information (reference sequence, position, errors, ...) by writing it in the FASTA read description." /> 217 <param name="desc_track" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Read tracking" help="Track read information (reference sequence, position, errors, ...) by writing it in the FASTA read description." />
215 218
216 <param name="qual_levels" type="text" optional="true" label="Quality score levels" help="Generate basic quality scores for the simulated reads. Good residues are given a specified good score (e.g. 30) and residues that are the result of an insertion or substitution are given a specified bad score (e.g. 10). Specify first the good score and then the bad score, e.g. '30 10'" /> 219 <param name="qual_levels" type="text" optional="true" label="Quality score levels" help="Generate basic quality scores for the simulated reads. Good residues are given a specified good score (e.g. 30) and residues that are the result of an insertion or substitution are given a specified bad score (e.g. 10). Specify first the good score and then the bad score, e.g. '30 10'" />
217 220
221 <param name="fastq_output" type="boolean" truevalue="1" falsevalue="0" checked="false" label="FASTQ output" help="
222 Write the generated reads in FASTQ format (Sanger variant) instead of FASTA and
223 QUAL. Quality score levels need to be specified for this option to be effective." />
224
218 <param name="profile_file" type="data" format="txt" optional="true" label="Profile file" help="A file that contains Grinder arguments. This is useful if you use many options or often use the same options. Lines with comments (#) are ignored. Consider the profile file, 'simple_profile.txt': 225 <param name="profile_file" type="data" format="txt" optional="true" label="Profile file" help="A file that contains Grinder arguments. This is useful if you use many options or often use the same options. Lines with comments (#) are ignored. Consider the profile file, 'simple_profile.txt':
219 226
220 # A simple Grinder profile 227 # A simple Grinder profile
221 -read_dist 105 normal 12 228 -read_dist 105 normal 12
222 -total_reads 1000 229 -total_reads 1000