Mercurial > repos > iuc > flash
comparison flash.xml @ 5:a27654fc4270 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31
author | iuc |
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date | Wed, 03 Apr 2019 19:49:20 -0400 |
parents | c85bdba47254 |
children | 01a4ebf1f237 |
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4:c85bdba47254 | 5:a27654fc4270 |
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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 |