Mercurial > repos > iuc > flash
diff flash.xml @ 2:b48895989d78 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5
| author | iuc |
|---|---|
| date | Thu, 19 Oct 2017 17:32:41 -0400 |
| parents | d043b54b3bfb |
| children | dce033fd3c80 |
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--- a/flash.xml Wed Oct 04 16:03:42 2017 -0400 +++ b/flash.xml Thu Oct 19 17:32:41 2017 -0400 @@ -1,12 +1,12 @@ <?xml version="1.0"?> -<tool id="flash" name="FLASH" version="@VERSION@.1"> +<tool id="flash" name="FLASH" version="@VERSION@.2"> <description>adjust length of short reads</description> + <macros> + <token name="@VERSION@">1.2.11</token> + </macros> <requirements> <requirement type="package" version="@VERSION@">flash</requirement> </requirements> - <macros> - <token name="@VERSION@">1.2.11</token> - </macros> <version_command>flash --version | head -n 1</version_command> <command detect_errors="aggressive"> <![CDATA[ @@ -17,23 +17,30 @@ $allow_outies #if $layout.select_layout == 'individual': '$layout.forward' '$layout.reverse' + #set $input = $layout.forward #else: '$layout.reads.forward' '$layout.reads.reverse' + #set $input = $layout.reads.forward + #end if + #if $input.dataset.extension == 'fastqsanger': + -p 33 + #else: + -p 64 #end if ]]> </command> <inputs> <conditional name="layout"> - <param name="select_layout" type="select"> + <param name="select_layout" type="select" label="Input data structure"> <option value="individual">Individual datasets</option> <option value="collection">Paired collection</option> </param> <when value="individual"> - <param format="fastq" name="forward" type="data" label="Forward reads" /> - <param format="fastq" name="reverse" type="data" label="Reverse reads" /> + <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" /> + <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" /> </when> <when value="collection"> - <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Read collection" /> + <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> </when> </conditional> <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." /> @@ -43,44 +50,61 @@ <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" /> </inputs> <outputs> - <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" /> - <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" /> - <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" /> + <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads"> + <filter>layout['select_layout'] == 'collection'</filter> + </data> + <data format_source="reads['forward']" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads"> + <filter>layout['select_layout'] == 'collection'</filter> + </data> + <data format_source="reads['reverse']" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads"> + <filter>layout['select_layout'] == 'collection'</filter> + </data> + <data format_source="forward" name="merged_paired_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads"> + <filter>layout['select_layout'] == 'individual'</filter> + </data> + <data format_source="forward" name="unmerged_paired_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads"> + <filter>layout['select_layout'] == 'individual'</filter> + </data> + <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads"> + <filter>layout['select_layout'] == 'individual'</filter> + </data> <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram"> <filter>generate_histogram</filter> </data> - <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" > + <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)"> <filter>allow_outies</filter> </data> - <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" > + <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)"> <filter>allow_outies</filter> </data> - <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" > + <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)"> <filter>allow_outies and generate_histogram</filter> </data> - <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" > + <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)"> <filter>allow_outies and generate_histogram</filter> </data> </outputs> <tests> <test> - <param name="forward" value="flash_forward_in1.fastq" /> - <param name="reverse" value="flash_reverse_in1.fastq" /> + <param name="select_layout" value="individual" /> + <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" /> + <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" /> <param name="generate_histogram" value="false" /> - <output name="merged_reads" file="flash_merged_out1.fastq" /> - <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" /> - <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" /> + <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" /> + <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" /> + <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" /> <output name="hist" file="flash_hist_out1.tabular" /> </test> <test> - <param name="forward" value="flash_forward_in2.fastq" /> - <param name="reverse" value="flash_reverse_in2.fastq" /> + <param name="select_layout" value="individual" /> + <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" /> + <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" /> <param name="allow_outies" value="true" /> <param name="generate_histogram" value="true" /> - <output name="merged_reads" file="flash_merged_out2.fastq" /> - <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" /> - <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" /> + <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" /> + <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" /> + <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" /> <output name="hist" file="flash_hist_out2.tabular" /> <output name="histogram" file="flash_hist_out2.txt" /> <output name="hist_in" file="flash_hist_in_out2.tabular" /> @@ -88,6 +112,20 @@ <output name="hist_out" file="flash_hist_out_out2.tabular" /> <output name="histogram_out" file="flash_hist_out_out2.txt" /> </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_in3.fastqillumina" ftype="fastqillumina" /> + <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" /> + </collection> + </param> + <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" /> + <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" /> + <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" /> + <output name="hist" file="flash_hist_out3.tabular" /> + </test> </tests> <help> <![CDATA[ @@ -108,4 +146,4 @@ <citations> <citation type="doi">10.1093/bioinformatics/btr507</citation> </citations> -</tool> \ No newline at end of file +</tool>