| Previous changeset 19:49370cb85f0f (2018-12-18) Next changeset 21:104d86c98776 (2020-03-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8 |
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modified:
cutadapt.xml macros.xml |
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added:
test-data/cutadapt_trimmed.out test-data/cutadapt_trimmed.out.gz test-data/cutadapt_untrimmed.out test-data/cutadapt_untrimmed.out.gz |
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| diff -r 49370cb85f0f -r e4691e1589d3 cutadapt.xml --- a/cutadapt.xml Tue Dec 18 14:09:53 2018 -0500 +++ b/cutadapt.xml Mon Apr 08 13:49:22 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09"> +<tool id="cutadapt" name="Cutadapt" version="1.16.6" profile="17.09"> <description>Remove adapter sequences from Fastq/Fasta</description> <macros> <import>macros.xml</import> @@ -35,34 +35,38 @@ #end if #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = $read1 + ".fq.gz" - #set out1 = "out1.gz" + #set ext = ".fq.gz" #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = $read1 + ".fq.bz2" - #set out1 = "out1.bz2" + #set ext = ".fq.bz2" #else if $input_1.is_of_type('fasta'): - #set read1 = $read1 + ".fa" - #set out1 = "out1.fa" + #set ext = ".fa" #else: - #set read1 = $read1 + ".fq" - #set out1 = "out1.fq" + #set ext = ".fq" #end if +#set read1 = $read1 + $ext +#set out1 = "out1" + $ext +#set rest_output = "rest_output" + $ext +#set wild_output = "wild_output" + $ext +#set too_short_output = "too_short_output" + $ext +#set too_long_output = "too_long_output" + $ext +#set untrimmed_output = "untrimmed_output" + $ext ln -f -s '${input_1}' '$read1' && #if $paired: #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read2 = $read2 + ".fq.gz" - #set out2 = "out2.gz" + #set ext2 = ".fq.gz" #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read2 = $read2 + ".fq.bz2" - #set out2 = "out2.bz2" + #set ext2 = ".fq.gz" #else if $input_2.is_of_type('fasta'): - #set read2 = $read2 + ".fa" - #set out2 = "out2.fa" + #set ext2 = ".fa" #else: - #set read2 = $read2 + ".fq" - #set out2 = "out2.fq" + #set ext2 = ".fq" #end if + #set read2 = $read2 + $ext2 + #set out2 = "out2" + $ext2 + #set too_short_paired_output = "too_short_paired_output" + $ext2 + #set too_long_paired_output = "too_long_paired_output" + $ext2 + #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2 ln -f -s '${input_2}' '$read2' && #end if @@ -252,40 +256,40 @@ <filter>(output_options['info_file'] is True)</filter> </data> - <data name="rest_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" > + <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" > <filter>(output_options['rest_file'] is True)</filter> <expand macro="inherit_format_1" /> </data> - <data name="wild_output" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Wildcard File" > + <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" > <filter>(output_options['wildcard_file'] is True)</filter> </data> - <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Untrimmed Read 1" > + <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" > <filter>(output_options['untrimmed_file'] is True)</filter> <expand macro="inherit_format_1" /> </data> - <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Untrimmed Read 2" > + <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" > <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> <filter>(output_options['untrimmed_file'] is True)</filter> <expand macro="inherit_format_2" /> </data> - <data name="too_short_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Short Read 1" > + <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" > <filter>(output_options['too_short_file'] is True)</filter> <expand macro="inherit_format_1" /> </data> - <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Short Read 2" > + <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" > <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> <filter>(output_options['too_short_file'] is True)</filter> <expand macro="inherit_format_2" /> </data> - <data name="too_long_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Long Read 1" > + <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" > <filter>(output_options['too_long_file'] is True)</filter> <expand macro="inherit_format_1" /> </data> - <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Long Read 2" > + <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" > <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> <filter>(output_options['too_long_file'] is True)</filter> <expand macro="inherit_format_2" /> @@ -463,6 +467,32 @@ </output_collection> </test> + <!-- Ensure untrimmed file output works --> + <test> + <param name="type" value="single" /> + <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AAAT"/> + <param name="untrimmed_file" value="True" /> + <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/> + <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/> + </test> + <!-- Ensure untrimmed gzip file output works --> + <test> + <param name="type" value="single" /> + <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AGATCGGAAGAGC"/> + <param name="untrimmed_file" value="True" /> + <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/> + <!-- + Do not use the decompress option for this assertion, since it does NOT test that the file is compressed + See discussion at https://github.com/galaxyproject/galaxy/issues/7671 + `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the + difference between level 1 compression and no compression + --> + <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/> + </test> </tests> <help><![CDATA[ |
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| diff -r 49370cb85f0f -r e4691e1589d3 macros.xml --- a/macros.xml Tue Dec 18 14:09:53 2018 -0500 +++ b/macros.xml Mon Apr 08 13:49:22 2019 -0400 |
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| @@ -48,19 +48,19 @@ --info-file=$info_file #end if #if $output_options.rest_file: - --rest-file=$rest_output + --rest-file='${rest_output}' #end if #if $output_options.wildcard_file: - --wildcard-file=$wild_output + --wildcard-file='${wild_output}' #end if #if $output_options.too_short_file: - --too-short-output=$too_short_output + --too-short-output='${too_short_output}' #end if #if $output_options.too_long_file: - --too-long-output=$too_long_output + --too-long-output='${too_long_output}' #end if #if $output_options.untrimmed_file: - --untrimmed-output=$untrimmed_output + --untrimmed-output='${untrimmed_output}' #end if ]]></token> @@ -110,13 +110,13 @@ ## Additional Outputs - Read 2 #if $output_options.too_short_file: - --too-short-paired-output=$too_short_paired_output + --too-short-paired-output='${too_short_paired_output}' #end if #if $output_options.too_long_file: - --too-long-paired-output=$too_long_paired_output + --too-long-paired-output='${too_long_paired_output}' #end if #if $output_options.untrimmed_file: - --untrimmed-paired-output=$untrimmed_paired_output + --untrimmed-paired-output='${untrimmed_paired_output}' #end if ]]></token> |
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| diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_trimmed.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_trimmed.out Mon Apr 08 13:49:22 2019 -0400 |
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| @@ -0,0 +1,4 @@ +@prefix:1_13_573/1 +CGTCCGAANTAGCTACCACCCTGATTAGAC ++ +)3%)&&&&!.1&(6:<'67..*,:75)'77 |
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| diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_trimmed.out.gz |
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| Binary file test-data/cutadapt_trimmed.out.gz has changed |
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| diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_untrimmed.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_untrimmed.out Mon Apr 08 13:49:22 2019 -0400 |
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| @@ -0,0 +1,8 @@ +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: |
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| diff -r 49370cb85f0f -r e4691e1589d3 test-data/cutadapt_untrimmed.out.gz |
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| Binary file test-data/cutadapt_untrimmed.out.gz has changed |