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comparison tools/seq_filter_by_mapping/seq_filter_by_mapping.xml @ 1:8ff0ac66f1a3 draft

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v0.0.4; Report FASTQ counts; misc internal changes
author peterjc
date Wed, 13 May 2015 11:08:58 -0400
parents 1d773da0ccf0
children 48e71dfd51b3
comparison
equal deleted inserted replaced
0:1d773da0ccf0 1:8ff0ac66f1a3
1 <tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.2"> 1 <tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.4">
2 <description>from SAM/BAM file</description> 2 <description>from SAM/BAM file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.64">biopython</requirement> 4 <requirement type="package" version="1.64">biopython</requirement>
5 <requirement type="python-module">Bio</requirement> 5 <requirement type="python-module">Bio</requirement>
6 <requirement type="binary">samtools</requirement> 6 <requirement type="binary">samtools</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement> 7 <requirement type="package" version="0.1.19">samtools</requirement>
8 </requirements> 8 </requirements>
9 <stdio>
10 <!-- Anything other than zero is an error -->
11 <exit_code range="1:" />
12 <exit_code range=":-1" />
13 </stdio>
9 <version_command interpreter="python">seq_filter_by_mapping.py --version</version_command> 14 <version_command interpreter="python">seq_filter_by_mapping.py --version</version_command>
10 <command interpreter="python"> 15 <command interpreter="python">
11 seq_filter_by_mapping.py -i "$input_file" -f "$input_file.ext" -m $pair_mode 16 seq_filter_by_mapping.py -i "$input_file" -f "$input_file.ext" -m $pair_mode
12 #if $output_choice_cond.output_choice=="both" 17 #if $output_choice_cond.output_choice=="both"
13 -p $output_pos -n $output_neg 18 -p $output_pos -n $output_neg
17 -n $output_neg 22 -n $output_neg
18 #end if 23 #end if
19 ## Now loop over all the mapping files 24 ## Now loop over all the mapping files
20 #for i in $mapping_file#${i} #end for# 25 #for i in $mapping_file#${i} #end for#
21 </command> 26 </command>
22 <stdio>
23 <!-- Anything other than zero is an error -->
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <inputs> 27 <inputs>
28 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> 28 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
29 <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." /> 29 <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." />
30 <conditional name="output_choice_cond"> 30 <conditional name="output_choice_cond">
31 <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?"> 31 <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?">
45 <option value="solo">Treat independently (will split partners when only one maps)</option> 45 <option value="solo">Treat independently (will split partners when only one maps)</option>
46 --> 46 -->
47 </param> 47 </param>
48 </inputs> 48 </inputs>
49 <outputs> 49 <outputs>
50 <data name="output_pos" format="input" metadata_source="input_file" label="$input_file.name (mapped)"> 50 <data name="output_pos" format_source="input_file" metadata_source="input_file" label="$input_file.name (mapped)">
51 <filter>output_choice_cond["output_choice"] != "neg"</filter> 51 <filter>output_choice_cond["output_choice"] != "neg"</filter>
52 </data> 52 </data>
53 <data name="output_neg" format="input" metadata_source="input_file" label="$input_file.name (unmapped)"> 53 <data name="output_neg" format_source="input_file" metadata_source="input_file" label="$input_file.name (unmapped)">
54 <filter>output_choice_cond["output_choice"] != "pos"</filter> 54 <filter>output_choice_cond["output_choice"] != "pos"</filter>
55 </data> 55 </data>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>