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comparison flash.xml @ 5:7dd535e8696b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
author iuc
date Wed, 03 Apr 2019 19:48:50 -0400
parents 2d05af94d290
children 147eae9635ec
comparison
equal deleted inserted replaced
4:2d05af94d290 5:7dd535e8696b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="flash" name="FLASH" version="@VERSION@.3"> 2 <tool id="flash" name="FLASH" version="@VERSION@.4">
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>
20 #set $input = $layout.forward 20 #set $input = $layout.forward
21 #else: 21 #else:
22 '$layout.reads.forward' '$layout.reads.reverse' 22 '$layout.reads.forward' '$layout.reads.reverse'
23 #set $input = $layout.reads.forward 23 #set $input = $layout.reads.forward
24 #end if 24 #end if
25 #if $input.is_of_type('fastqsanger'): 25 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz'):
26 -p 33 26 -p 33
27 #else: 27 #else:
28 -p 64 28 -p 64
29 #end if 29 #end if
30 30 #if $input.ext.endswith('.gz'):
31 -z
32 #end if
33 --output-suffix=''
31 #if $save_log: 34 #if $save_log:
32 > '$log' 35 > '$log'
33 #end if 36 #end if
34 ]]> 37 ]]>
35 </command> 38 </command>
38 <param name="select_layout" type="select" label="Input data structure"> 41 <param name="select_layout" type="select" label="Input data structure">
39 <option value="individual">Individual datasets</option> 42 <option value="individual">Individual datasets</option>
40 <option value="collection">Paired collection</option> 43 <option value="collection">Paired collection</option>
41 </param> 44 </param>
42 <when value="individual"> 45 <when value="individual">
43 <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" /> 46 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="forward" type="data" label="Forward reads" />
44 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" /> 47 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reverse" type="data" label="Reverse reads" />
45 </when> 48 </when>
46 <when value="collection"> 49 <when value="collection">
47 <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> 50 <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
48 </when> 51 </when>
49 </conditional> 52 </conditional>
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." /> 53 <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." />
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." /> 54 <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." />
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." /> 55 <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." />
143 </param> 146 </param>
144 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" /> 147 <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
145 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" /> 148 <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
146 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" /> 149 <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
147 <output name="hist" file="flash_hist_out3.tabular" /> 150 <output name="hist" file="flash_hist_out3.tabular" />
151 </test>
152 <test>
153 <param name="select_layout" value="individual" />
154 <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
155 <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
156 <param name="generate_histogram" value="false" />
157 <param name="save_log" value="true" />
158 <output name="merged_paired_reads" file="flash_merged_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
159 <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
160 <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
161 <output name="log">
162 <assert_contents>
163 <has_line_matching expression=".*Percent combined: 3.60%" />
164 </assert_contents>
165 </output>
166 </test>
167 <test>
168 <param name="select_layout" value="collection" />
169 <param name="generate_histogram" value="false" />
170 <param name="reads">
171 <collection type="paired">
172 <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
173 <element name="reverse" value="flash_reverse_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
174 </collection>
175 </param>
176 <output name="merged_reads" file="flash_merged_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
177 <output name="unmerged_reads_f" file="flash_unmerged_f_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
178 <output name="unmerged_reads_r" file="flash_unmerged_r_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
179 <output name="hist" file="flash_hist_out5.tabular" />
148 </test> 180 </test>
149 </tests> 181 </tests>
150 <help> 182 <help>
151 <![CDATA[ 183 <![CDATA[
152 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool 184 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool