| Previous changeset 4:c85bdba47254 (2019-04-01) Next changeset 6:01a4ebf1f237 (2022-07-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31 |
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modified:
flash.xml |
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added:
test-data/flash_forward_in4.fastqsanger.gz test-data/flash_forward_in5.fastqsanger.gz test-data/flash_hist_out5.tabular test-data/flash_merged_out4.fastqsanger.gz test-data/flash_merged_out5.fastqsanger.gz test-data/flash_reverse_in4.fastqsanger.gz test-data/flash_reverse_in5.fastqsanger.gz test-data/flash_unmerged_f_out4.fastqsanger.gz test-data/flash_unmerged_f_out5.fastqsanger.gz test-data/flash_unmerged_r_out4.fastqsanger.gz test-data/flash_unmerged_r_out5.fastqsanger.gz |
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| diff -r c85bdba47254 -r a27654fc4270 flash.xml --- a/flash.xml Mon Apr 01 19:01:31 2019 -0400 +++ b/flash.xml Wed Apr 03 19:49:20 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="flash" name="FLASH" version="@VERSION@.3"> +<tool id="flash" name="FLASH" version="@VERSION@.4"> <description>adjust length of short reads</description> <macros> <token name="@VERSION@">1.2.11</token> @@ -22,12 +22,15 @@ '$layout.reads.forward' '$layout.reads.reverse' #set $input = $layout.reads.forward #end if - #if $input.is_of_type('fastqsanger'): + #if $input.is_of_type('fastqsanger', 'fastqsanger.gz'): -p 33 #else: -p 64 #end if - + #if $input.ext.endswith('.gz'): + -z + #end if + --output-suffix='' #if $save_log: > '$log' #end if @@ -40,11 +43,11 @@ <option value="collection">Paired collection</option> </param> <when value="individual"> - <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" /> - <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" /> + <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="forward" type="data" label="Forward reads" /> + <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reverse" type="data" label="Reverse reads" /> </when> <when value="collection"> - <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> + <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> </when> </conditional> <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." /> @@ -146,6 +149,35 @@ <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" /> <output name="hist" file="flash_hist_out3.tabular" /> </test> + <test> + <param name="select_layout" value="individual" /> + <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> + <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" /> + <param name="generate_histogram" value="false" /> + <param name="save_log" value="true" /> + <output name="merged_paired_reads" file="flash_merged_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="log"> + <assert_contents> + <has_line_matching expression=".*Percent combined: 3.60%" /> + </assert_contents> + </output> + </test> + <test> + <param name="select_layout" value="collection" /> + <param name="generate_histogram" value="false" /> + <param name="reads"> + <collection type="paired"> + <element name="forward" value="flash_forward_in5.fastqsanger.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="flash_reverse_in5.fastqsanger.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + <output name="merged_reads" file="flash_merged_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="unmerged_reads_f" file="flash_unmerged_f_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="unmerged_reads_r" file="flash_unmerged_r_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" /> + <output name="hist" file="flash_hist_out5.tabular" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r c85bdba47254 -r a27654fc4270 test-data/flash_hist_out5.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flash_hist_out5.tabular Wed Apr 03 19:49:20 2019 -0400 |
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| @@ -0,0 +1,14 @@ +352 1 +367 1 +368 2 +370 1 +374 1 +375 1 +376 2 +377 1 +379 1 +382 1 +383 1 +385 1 +386 1 +388 3 |
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