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comparison flash.xml @ 2:40cec756baa4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Thu, 19 Oct 2017 17:32:20 -0400
parents 7f7be04e2172
children e426928f1572
comparison
equal deleted inserted replaced
1:7f7be04e2172 2:40cec756baa4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="flash" name="FLASH" version="@VERSION@.1"> 2 <tool id="flash" name="FLASH" version="@VERSION@.2">
3 <description>adjust length of short reads</description> 3 <description>adjust length of short reads</description>
4 <macros>
5 <token name="@VERSION@">1.2.11</token>
6 </macros>
4 <requirements> 7 <requirements>
5 <requirement type="package" version="@VERSION@">flash</requirement> 8 <requirement type="package" version="@VERSION@">flash</requirement>
6 </requirements> 9 </requirements>
7 <macros>
8 <token name="@VERSION@">1.2.11</token>
9 </macros>
10 <version_command>flash --version | head -n 1</version_command> 10 <version_command>flash --version | head -n 1</version_command>
11 <command detect_errors="aggressive"> 11 <command detect_errors="aggressive">
12 <![CDATA[ 12 <![CDATA[
13 flash --threads=\${GALAXY_SLOTS:-1} 13 flash --threads=\${GALAXY_SLOTS:-1}
14 -m $min_overlap 14 -m $min_overlap
15 -M $max_overlap 15 -M $max_overlap
16 -x $max_mismatch_density 16 -x $max_mismatch_density
17 $allow_outies 17 $allow_outies
18 #if $layout.select_layout == 'individual': 18 #if $layout.select_layout == 'individual':
19 '$layout.forward' '$layout.reverse' 19 '$layout.forward' '$layout.reverse'
20 #set $input = $layout.forward
20 #else: 21 #else:
21 '$layout.reads.forward' '$layout.reads.reverse' 22 '$layout.reads.forward' '$layout.reads.reverse'
23 #set $input = $layout.reads.forward
24 #end if
25 #if $input.dataset.extension == 'fastqsanger':
26 -p 33
27 #else:
28 -p 64
22 #end if 29 #end if
23 ]]> 30 ]]>
24 </command> 31 </command>
25 <inputs> 32 <inputs>
26 <conditional name="layout"> 33 <conditional name="layout">
27 <param name="select_layout" type="select"> 34 <param name="select_layout" type="select" label="Input data structure">
28 <option value="individual">Individual datasets</option> 35 <option value="individual">Individual datasets</option>
29 <option value="collection">Paired collection</option> 36 <option value="collection">Paired collection</option>
30 </param> 37 </param>
31 <when value="individual"> 38 <when value="individual">
32 <param format="fastq" name="forward" type="data" label="Forward reads" /> 39 <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" />
33 <param format="fastq" name="reverse" type="data" label="Reverse reads" /> 40 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" />
34 </when> 41 </when>
35 <when value="collection"> 42 <when value="collection">
36 <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Read collection" /> 43 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
37 </when> 44 </when>
38 </conditional> 45 </conditional>
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." /> 46 <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." />
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." /> 47 <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." />
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." /> 48 <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." />
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." /> 49 <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" /> 50 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
44 </inputs> 51 </inputs>
45 <outputs> 52 <outputs>
46 <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" /> 53 <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
47 <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" /> 54 <filter>layout['select_layout'] == 'collection'</filter>
48 <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" /> 55 </data>
56 <data format_source="reads['forward']" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
57 <filter>layout['select_layout'] == 'collection'</filter>
58 </data>
59 <data format_source="reads['reverse']" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
60 <filter>layout['select_layout'] == 'collection'</filter>
61 </data>
62 <data format_source="forward" name="merged_paired_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
63 <filter>layout['select_layout'] == 'individual'</filter>
64 </data>
65 <data format_source="forward" name="unmerged_paired_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
66 <filter>layout['select_layout'] == 'individual'</filter>
67 </data>
68 <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
69 <filter>layout['select_layout'] == 'individual'</filter>
70 </data>
49 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> 71 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
50 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram"> 72 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
51 <filter>generate_histogram</filter> 73 <filter>generate_histogram</filter>
52 </data> 74 </data>
53 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" > 75 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)">
54 <filter>allow_outies</filter> 76 <filter>allow_outies</filter>
55 </data> 77 </data>
56 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" > 78 <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)">
57 <filter>allow_outies</filter> 79 <filter>allow_outies</filter>
58 </data> 80 </data>
59 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" > 81 <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)">
60 <filter>allow_outies and generate_histogram</filter> 82 <filter>allow_outies and generate_histogram</filter>
61 </data> 83 </data>
62 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" > 84 <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
63 <filter>allow_outies and generate_histogram</filter> 85 <filter>allow_outies and generate_histogram</filter>
64 </data> 86 </data>
65 </outputs> 87 </outputs>
66 <tests> 88 <tests>
67 <test> 89 <test>
68 <param name="forward" value="flash_forward_in1.fastq" /> 90 <param name="select_layout" value="individual" />
69 <param name="reverse" value="flash_reverse_in1.fastq" /> 91 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
92 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
70 <param name="generate_histogram" value="false" /> 93 <param name="generate_histogram" value="false" />
71 <output name="merged_reads" file="flash_merged_out1.fastq" /> 94 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
72 <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" /> 95 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
73 <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" /> 96 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
74 <output name="hist" file="flash_hist_out1.tabular" /> 97 <output name="hist" file="flash_hist_out1.tabular" />
75 </test> 98 </test>
76 <test> 99 <test>
77 <param name="forward" value="flash_forward_in2.fastq" /> 100 <param name="select_layout" value="individual" />
78 <param name="reverse" value="flash_reverse_in2.fastq" /> 101 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
102 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
79 <param name="allow_outies" value="true" /> 103 <param name="allow_outies" value="true" />
80 <param name="generate_histogram" value="true" /> 104 <param name="generate_histogram" value="true" />
81 <output name="merged_reads" file="flash_merged_out2.fastq" /> 105 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
82 <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" /> 106 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
83 <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" /> 107 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
84 <output name="hist" file="flash_hist_out2.tabular" /> 108 <output name="hist" file="flash_hist_out2.tabular" />
85 <output name="histogram" file="flash_hist_out2.txt" /> 109 <output name="histogram" file="flash_hist_out2.txt" />
86 <output name="hist_in" file="flash_hist_in_out2.tabular" /> 110 <output name="hist_in" file="flash_hist_in_out2.tabular" />
87 <output name="histogram_in" file="flash_hist_in_out2.txt" /> 111 <output name="histogram_in" file="flash_hist_in_out2.txt" />
88 <output name="hist_out" file="flash_hist_out_out2.tabular" /> 112 <output name="hist_out" file="flash_hist_out_out2.tabular" />
89 <output name="histogram_out" file="flash_hist_out_out2.txt" /> 113 <output name="histogram_out" file="flash_hist_out_out2.txt" />
114 </test>
115 <test>
116 <param name="select_layout" value="collection" />
117 <param name="generate_histogram" value="false" />
118 <param name="reads">
119 <collection type="paired">
120 <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
121 <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
122 </collection>
123 </param>
124 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
125 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
126 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
127 <output name="hist" file="flash_hist_out3.tabular" />
90 </test> 128 </test>
91 </tests> 129 </tests>
92 <help> 130 <help>
93 <![CDATA[ 131 <![CDATA[
94 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool 132 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool