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comparison flash.xml @ 1:7f7be04e2172 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit cac63023973d851956b967df436be91aa8729f2e
author iuc
date Wed, 04 Oct 2017 16:03:25 -0400
parents a8e42976aa6b
children 40cec756baa4
comparison
equal deleted inserted replaced
0:a8e42976aa6b 1:7f7be04e2172
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="flash" name="FLASH" version="1.2.11"> 2 <tool id="flash" name="FLASH" version="@VERSION@.1">
3 <description>adjust length of short reads</description> 3 <description>adjust length of short reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.11">flash</requirement> 5 <requirement type="package" version="@VERSION@">flash</requirement>
6 </requirements> 6 </requirements>
7 <macros>
8 <token name="@VERSION@">1.2.11</token>
9 </macros>
7 <version_command>flash --version | head -n 1</version_command> 10 <version_command>flash --version | head -n 1</version_command>
8 <command detect_errors="aggressive"> 11 <command detect_errors="aggressive">
9 <![CDATA[ 12 <![CDATA[
10 flash --threads=\${GALAXY_SLOTS:-1} 13 flash --threads=\${GALAXY_SLOTS:-1}
11 -m $min_overlap 14 -m $min_overlap
12 -M $max_overlap 15 -M $max_overlap
13 -x $max_mismatch_density 16 -x $max_mismatch_density
14 $allow_outies 17 $allow_outies
15 '$forward' '$reverse' 18 #if $layout.select_layout == 'individual':
19 '$layout.forward' '$layout.reverse'
20 #else:
21 '$layout.reads.forward' '$layout.reads.reverse'
22 #end if
16 ]]> 23 ]]>
17 </command> 24 </command>
18 <inputs> 25 <inputs>
19 <param format="fastq" name="forward" type="data" label="Forward reads" /> 26 <conditional name="layout">
20 <param format="fastq" name="reverse" type="data" label="Reverse reads" /> 27 <param name="select_layout" type="select">
28 <option value="individual">Individual datasets</option>
29 <option value="collection">Paired collection</option>
30 </param>
31 <when value="individual">
32 <param format="fastq" name="forward" type="data" label="Forward reads" />
33 <param format="fastq" name="reverse" type="data" label="Reverse reads" />
34 </when>
35 <when value="collection">
36 <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Read collection" />
37 </when>
38 </conditional>
21 <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." /> 39 <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
22 <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." /> 40 <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
23 <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." /> 41 <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
24 <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." /> 42 <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
43 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
25 </inputs> 44 </inputs>
26 <outputs> 45 <outputs>
27 <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" /> 46 <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" />
28 <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" /> 47 <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" />
29 <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" /> 48 <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" />
30 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> 49 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
31 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram" /> 50 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
51 <filter>generate_histogram</filter>
52 </data>
32 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" > 53 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" >
33 <filter>allow_outies</filter> 54 <filter>allow_outies</filter>
34 </data> 55 </data>
35 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" > 56 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" >
36 <filter>allow_outies</filter> 57 <filter>allow_outies</filter>
37 </data> 58 </data>
38 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" > 59 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" >
39 <filter>allow_outies</filter> 60 <filter>allow_outies and generate_histogram</filter>
40 </data> 61 </data>
41 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" > 62 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" >
42 <filter>allow_outies</filter> 63 <filter>allow_outies and generate_histogram</filter>
43 </data> 64 </data>
44 </outputs> 65 </outputs>
45 <tests> 66 <tests>
46 <test> 67 <test>
47 <param name="forward" value="flash_forward_in1.fastq" /> 68 <param name="forward" value="flash_forward_in1.fastq" />
48 <param name="reverse" value="flash_reverse_in1.fastq" /> 69 <param name="reverse" value="flash_reverse_in1.fastq" />
70 <param name="generate_histogram" value="false" />
49 <output name="merged_reads" file="flash_merged_out1.fastq" /> 71 <output name="merged_reads" file="flash_merged_out1.fastq" />
50 <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" /> 72 <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" />
51 <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" /> 73 <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" />
52 <output name="hist" file="flash_hist_out1.tabular" /> 74 <output name="hist" file="flash_hist_out1.tabular" />
53 <output name="histogram" file="flash_hist_out1.txt" />
54 </test> 75 </test>
55 <test> 76 <test>
56 <param name="forward" value="flash_forward_in2.fastq" /> 77 <param name="forward" value="flash_forward_in2.fastq" />
57 <param name="reverse" value="flash_reverse_in2.fastq" /> 78 <param name="reverse" value="flash_reverse_in2.fastq" />
58 <param name="allow_outies" value="true" /> 79 <param name="allow_outies" value="true" />
80 <param name="generate_histogram" value="true" />
59 <output name="merged_reads" file="flash_merged_out2.fastq" /> 81 <output name="merged_reads" file="flash_merged_out2.fastq" />
60 <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" /> 82 <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" />
61 <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" /> 83 <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" />
62 <output name="hist" file="flash_hist_out2.tabular" /> 84 <output name="hist" file="flash_hist_out2.tabular" />
63 <output name="histogram" file="flash_hist_out2.txt" /> 85 <output name="histogram" file="flash_hist_out2.txt" />