Mercurial > repos > iuc > flash

comparison flash.xml @ 3:e426928f1572 draft

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/flash commit 22bfb515121a4f18ccfa907b0a18c98028e7064e
author iuc
date Wed, 08 Nov 2017 11:05:39 -0500
parents 40cec756baa4
children 2d05af94d290
comparison
equal deleted inserted replaced
2:40cec756baa4 3:e426928f1572
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="flash" name="FLASH" version="@VERSION@.2"> 2 <tool id="flash" name="FLASH" version="@VERSION@.3">
3 <description>adjust length of short reads</description> 3 <description>adjust length of short reads</description>
4 <macros> 4 <macros>
5 <token name="@VERSION@">1.2.11</token> 5 <token name="@VERSION@">1.2.11</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
25 #if $input.dataset.extension == 'fastqsanger': 25 #if $input.dataset.extension == 'fastqsanger':
26 -p 33 26 -p 33
27 #else: 27 #else:
28 -p 64 28 -p 64
29 #end if 29 #end if
30
31 #if $save_log:
32 > '$log'
33 #end if
30 ]]> 34 ]]>
31 </command> 35 </command>
32 <inputs> 36 <inputs>
33 <conditional name="layout"> 37 <conditional name="layout">
34 <param name="select_layout" type="select" label="Input data structure"> 38 <param name="select_layout" type="select" label="Input data structure">
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." /> 50 <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." />
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." /> 51 <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." />
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." /> 52 <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." />
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." /> 53 <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." />
50 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" /> 54 <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
55 <param name="save_log" type="boolean" truevalue="" falsevalue="" checked="false" label="Save FLASH log file" />
51 </inputs> 56 </inputs>
52 <outputs> 57 <outputs>
53 <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads"> 58 <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
54 <filter>layout['select_layout'] == 'collection'</filter> 59 <filter>layout['select_layout'] == 'collection'</filter>
55 </data> 60 </data>
67 </data> 72 </data>
68 <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads"> 73 <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
69 <filter>layout['select_layout'] == 'individual'</filter> 74 <filter>layout['select_layout'] == 'individual'</filter>
70 </data> 75 </data>
71 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> 76 <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
77 <data format="txt" name="log" label="${tool.name} on ${on_string}: Raw Log">
78 <filter>raw_log == 'yes'</filter>
79 </data>
72 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram"> 80 <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
73 <filter>generate_histogram</filter> 81 <filter>generate_histogram</filter>
74 </data> 82 </data>
75 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)"> 83 <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)">
76 <filter>allow_outies</filter> 84 <filter>allow_outies</filter>
89 <test> 97 <test>
90 <param name="select_layout" value="individual" /> 98 <param name="select_layout" value="individual" />
91 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" /> 99 <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
92 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" /> 100 <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
93 <param name="generate_histogram" value="false" /> 101 <param name="generate_histogram" value="false" />
102 <param name="save_log" value="true" />
94 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" /> 103 <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
95 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" /> 104 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
96 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" /> 105 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
97 <output name="hist" file="flash_hist_out1.tabular" /> 106 <output name="hist" file="flash_hist_out1.tabular" />
107 <output name="log">
108 <assert_contents>
109 <has_line_matching expression=".*Percent combined: 3.60%" />
110 </assert_contents>
111 </output>
98 </test> 112 </test>
99 <test> 113 <test>
100 <param name="select_layout" value="individual" /> 114 <param name="select_layout" value="individual" />
101 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" /> 115 <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
102 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" /> 116 <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
103 <param name="allow_outies" value="true" /> 117 <param name="allow_outies" value="true" />
104 <param name="generate_histogram" value="true" /> 118 <param name="generate_histogram" value="true" />
119 <param name="save_log" value="true" />
105 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" /> 120 <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
106 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" /> 121 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
107 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" /> 122 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
108 <output name="hist" file="flash_hist_out2.tabular" /> 123 <output name="hist" file="flash_hist_out2.tabular" />
109 <output name="histogram" file="flash_hist_out2.txt" /> 124 <output name="histogram" file="flash_hist_out2.txt" />
110 <output name="hist_in" file="flash_hist_in_out2.tabular" /> 125 <output name="hist_in" file="flash_hist_in_out2.tabular" />
111 <output name="histogram_in" file="flash_hist_in_out2.txt" /> 126 <output name="histogram_in" file="flash_hist_in_out2.txt" />
112 <output name="hist_out" file="flash_hist_out_out2.tabular" /> 127 <output name="hist_out" file="flash_hist_out_out2.tabular" />
113 <output name="histogram_out" file="flash_hist_out_out2.txt" /> 128 <output name="histogram_out" file="flash_hist_out_out2.txt" />
129 <output name="log">
130 <assert_contents>
131 <has_line_matching expression=".*Percent combined: 3.80%" />
132 </assert_contents>
133 </output>
114 </test> 134 </test>
115 <test> 135 <test>
116 <param name="select_layout" value="collection" /> 136 <param name="select_layout" value="collection" />
117 <param name="generate_histogram" value="false" /> 137 <param name="generate_histogram" value="false" />
118 <param name="reads"> 138 <param name="reads">