Mercurial > repos > iuc > sickle
changeset 5:3905ccd5c631 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
author | iuc |
---|---|
date | Thu, 13 Apr 2017 16:06:10 -0400 |
parents | edaa8572219d |
children | 6756c87dc2d4 |
files | sickle.xml test-data/output.c2.fastq test-data/output.f.fastq.gz test-data/output.r.fastq.gz test-data/output.s.fastq.gz test-data/test.f.fastq.gz test-data/test.r.fastq.gz |
diffstat | 7 files changed, 148 insertions(+), 76 deletions(-) [+] |
line wrap: on
line diff
--- a/sickle.xml Mon Jan 23 06:07:05 2017 -0500 +++ b/sickle.xml Thu Apr 13 16:06:10 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="sickle" name="Sickle" version="1.33"> +<tool id="sickle" name="Sickle" version="1.33.1" profile="17.01"> <description>windowed adaptive trimming of FASTQ data</description> <requirements> <requirement type="package" version="1.33">sickle</requirement> @@ -6,60 +6,106 @@ <requirement type="package" version="1.33">sickle-trim</requirement> </requirements> <version_command>sickle --version | head -n 1</version_command> - <command> + <command><![CDATA[ + ## Link in the input files, which also determines the type of the output + #set compressed = "" + #if str($readtype.single_or_paired) == "se": + #if $readtype.input_single.is_of_type('fastq.gz'): + #set read1 = "input_1.fastq.gz" + #set compressed = "-g" + #else + #set read1 = "input_1.fastq" + #end if + ln -f -s '${readtype.input_single}' ${read1} && + #else if str($readtype.single_or_paired) == "pe_combo": + #if $readtype.input_combo.is_of_type('fastq.gz'): + #set read1 = "input_1.fastq.gz" + #set compressed = "-g" + #else + #set read1 = "input_1.fastq" + #end if + ln -f -s '${readtype.input_combo}' ${read1} && + #else if str($readtype.single_or_paired) == "pe_sep": + #if $readtype.input_paired1.is_of_type('fastq.gz'): + #set read1 = "input_1.fastq.gz" + #set compressed = "-g" + #else + #set read1 = "input_1.fastq" + #end if + ln -f -s '${readtype.input_paired1}' ${read1} && + + #if $readtype.input_paired2.is_of_type('fastq.gz'): + #set read2 = "input_2.fastq.gz" + #else + #set read2 = "input_2.fastq" + #end if + ln -f -s '${readtype.input_paired2}' ${read2} && + #else + #if $readtype.input_paired.forward.is_of_type('fastq.gz'): + #set read1 = "input_1.fastq.gz" + #set compressed = "-g" + #else + #set read1 = "input_1.fastq" + #end if + ln -f -s '${readtype.input_paired.forward}' ${read1} && + + #if $readtype.input_paired.reverse.is_of_type('fastq.gz'): + #set read2 = "input_2.fastq.gz" + #else + #set read2 = "input_2.fastq" + #end if + ln -f -s '${readtype.input_paired.reverse}' ${read2} && + #end if + sickle #if str($readtype.single_or_paired) == "se": - se -f "${readtype.input_single}" -o "$output_single" + se -f ${read1} -o '${output_single}' + + #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'): + -t illumina + #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'): + -t solexa + #else: + -t sanger + #end if + #else if str($readtype.single_or_paired) == "pe_combo": + #if $readtype.output_n: + pe -c ${read1} -M '${output_combo}' + #else + pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}' + #end if - #if $readtype.input_single.is_of_type('fastqillumina'): + #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'): + -t illumina + #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'): + -t solexa + #else: + -t sanger + #end if + #else if str($readtype.single_or_paired) == "pe_sep": + pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}' + + #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'): -t illumina - #else if $readtype.input_single.is_of_type('fastqsolexa'): + #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'): + -t solexa + #else: + -t sanger + #end if + #else if str($readtype.single_or_paired) == "pe_collection": + pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}' + + #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'): + -t illumina + #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'): -t solexa #else: -t sanger #end if #end if - #if str($readtype.single_or_paired) == "pe_combo": - #if $readtype.output_n: - pe -c "${readtype.input_combo}" -M "$output_combo" - #else - pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single" - #end if - - #if $readtype.input_combo.is_of_type('fastqillumina'): - -t illumina - #else if $readtype.input_combo.is_of_type('fastqsolexa'): - -t solexa - #else: - -t sanger - #end if - #end if - - #if str($readtype.single_or_paired) == "pe_sep": - pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single" - - #if $readtype.input_paired1.is_of_type('fastqillumina'): - -t illumina - #else if $readtype.input_paired1.is_of_type('fastqsolexa'): - -t solexa - #else: - -t sanger - #end if - #end if - - #if str($readtype.single_or_paired) == "pe_collection": - pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single" - - #if $readtype.input_paired.forward.is_of_type('fastqillumina'): - -t illumina - #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'): - -t solexa - #else: - -t sanger - #end if - #end if + $compressed #if str($qual_threshold) != "": -q $qual_threshold @@ -76,6 +122,7 @@ #if $trunc_n: -n #end if + ]]> </command> <inputs> @@ -88,21 +135,21 @@ </param> <when value="se"> - <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" /> + <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" /> </when> <when value="pe_combo"> - <param format="fastq" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" /> + <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" /> <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/> </when> <when value="pe_sep"> - <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> - <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> + <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> + <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> </when> <when value="pe_collection"> - <param format="fastq" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" /> + <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" /> </when> </conditional> @@ -150,41 +197,66 @@ <tests> <test> <param name="single_or_paired" value="pe_combo" /> - <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> - <param name="qual_threshold" value="34" /> - <output name="output_combo" ftype="fastqsanger" file="output.c1.fastq" /> - <output name="output_combo_single" ftype="fastqsanger" file="output.s.fastq" /> + <param name="input_combo" ftype="fastqillumina" value="test.fastq" /> + <param name="qual_threshold" value="3" /> + <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq" /> + <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq" /> </test> <test> <param name="single_or_paired" value="pe_combo" /> - <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> - <param name="qual_threshold" value="34" /> + <param name="input_combo" ftype="fastqillumina" value="test.fastq" /> + <param name="qual_threshold" value="3" /> <param name="output_n" value="true" /> - <output name="output_combo" ftype="fastqsanger" file="output.c2.fastq" /> + <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq" /> </test> <test> <param name="single_or_paired" value="pe_sep" /> - <param name="input_paired1" ftype="fastqsanger" value="test.f.fastq" /> - <param name="input_paired2" ftype="fastqsanger" value="test.r.fastq" /> - <param name="qual_threshold" value="34" /> - <output name="output_paired1" ftype="fastqsanger" file="output.f.fastq" /> - <output name="output_paired2" ftype="fastqsanger" file="output.r.fastq" /> - <output name="output_paired_single" ftype="fastqsanger" file="output.s.fastq" /> + <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" /> + <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" /> + <param name="qual_threshold" value="3" /> + <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" /> + <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" /> + <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" /> + </test> + <test> <!-- as above, but gzipped --> + <param name="single_or_paired" value="pe_sep" /> + <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" /> + <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" /> + <param name="qual_threshold" value="3" /> + <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" /> + <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" /> + <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" /> </test> <test> <param name="single_or_paired" value="pe_collection" /> <param name="input_paired"> <collection type="paired"> - <element name="forward" ftype="fastqsanger" value="test.f.fastq" /> - <element name="reverse" ftype="fastqsanger" value="test.r.fastq" /> + <element name="forward" ftype="fastqillumina" value="test.f.fastq" /> + <element name="reverse" ftype="fastqillumina" value="test.r.fastq" /> </collection> </param> - <param name="qual_threshold" value="34" /> + <param name="qual_threshold" value="3" /> <output_collection name="output_paired_coll" type="paired"> - <element name="forward" ftype="fastqsanger" file="output.f.fastq" /> - <element name="reverse" ftype="fastqsanger" file="output.r.fastq" /> + <element name="forward" ftype="fastqillumina" file="output.f.fastq" /> + <element name="reverse" ftype="fastqillumina" file="output.r.fastq" /> </output_collection> - <output name="output_paired_coll_single" ftype="fastqsanger" file="output.s.fastq" /> + <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" /> + </test> + + <test> <!-- as above, but gzipped --> + <param name="single_or_paired" value="pe_collection" /> + <param name="input_paired"> + <collection type="paired"> + <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" /> + <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" /> + </collection> + </param> + <param name="qual_threshold" value="3" /> + <output_collection name="output_paired_coll" type="paired"> + <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" /> + <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" /> + </output_collection> + <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" /> </test> </tests> <help>
--- a/test-data/output.c2.fastq Mon Jan 23 06:07:05 2017 -0500 +++ b/test-data/output.c2.fastq Thu Apr 13 16:06:10 2017 -0400 @@ -1069,7 +1069,7 @@ @2242:2:1101:1410:2072/2 N + -! +@ @2242:2:1101:1341:2087/1 GCAAGGCTTGGATAATGTCACCTGTGCCAAGGAGGGCAATACCCAGCTGGTAGAAAACTGTTCCCTTATGTATTCCCCTATTCAGCNGAGTCTGGGCAC + @@ -1693,7 +1693,7 @@ @2242:2:1101:3714:2244/2 N + -! +@ @2242:2:1101:3917:2028/1 CCATTTCCTCGCTACGTATGATCCTGTGAATTACCAACTTCTCTCCCAGGGACCGCAGACATTGACGCTGAATTTGTTTGCCGGAATATCCCCGACGGACAACGGTGCAGCGCTTCTGGCCGCCGCCGAACGGGCAAGAGTGCAGTTGAA + @@ -2693,7 +2693,7 @@ @2242:2:1101:5866:2211/2 N + -! +@ @2242:2:1101:5804:2222/1 TCCCCGCTACCACCCCTGGCGGAACCACATTCTAGCAGACGGTCTGAAAGGTGTCGAGGCACAACTGACGACGGGCGCGAGACGCCCCGACAGGTTCGA + @@ -6053,7 +6053,7 @@ @2242:2:1101:14860:2072/2 N + -! +@ @2242:2:1101:14831:2097/1 ATCTTGAATCAGAACCATTTGGTTTTGGCTGCCCTTTCCTCGAAAGAATCCGTAACCGTCCCATCCGTTCACAGCGATACTATCCAGGTTGCTCAGGTCGACGATGAAGCAACCCAGGAGAAACCCCCCACAGA + @@ -6165,7 +6165,7 @@ @2242:2:1101:15244:2185/2 N + -! +@ @2242:2:1101:15156:2199/1 AGTTCCCTTGTATTGAATGGTATTATCCGGCGGCAGGTTTCCCCGCATAAGCGCCGCCCCGGCAATCGTTATCCGCAATAATAGCGGCGTCAGTATCCTGTTGTCGGCTATCAGGCAATTATATTGCCTCGACTCGCTGTCATTATACCG + @@ -9101,7 +9101,7 @@ @2242:2:1101:3440:2300/2 N + -! +@ @2242:2:1101:3379:2319/1 GAGGAAAAACGGTTAGCCGGGGGGCCTTCCCACTACTAGCCGTCGAGAAAATGCTTGATGAGGTAGTGGTAGATGTCCTTGCCGATTTGCATCCCCACCTCAATGATTTCCGGACCATACTGGCGTCCGGTGGCGGTGCGAAAGGGCTCT + @@ -9373,7 +9373,7 @@ @2242:2:1101:4206:2262/2 N + -! +@ @2242:2:1101:4230:2263/1 GAAAGCGTCGGCGGAAGTCGAAACAAGGCAGCCAAGCGTCTTGGAATCCATCGCAATACCCTGTTATCCAAGATATATTGCCTTAAAGAAATAGATAATAATATAAGTTAGTTACTGAATTCAATACATACTCAATTTTGTCCCTTGCTC + @@ -9429,7 +9429,7 @@ @2242:2:1101:4109:2339/2 N + -! +@ @2242:2:1101:4113:2360/1 GATTGCTGATCAGGGGGAAGGGATGAGAGACATCCACCGCGAGGGGCGTAAGGATAGGCTCCACCGATTTGCGGAAATACCGCTTCATCTGAGCGCGCTGGGACTTGTCCA +