| Previous changeset 4:edaa8572219d (2017-01-23) Next changeset 6:6756c87dc2d4 (2019-09-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 |
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modified:
sickle.xml test-data/output.c2.fastq |
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added:
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 |
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| diff -r edaa8572219d -r 3905ccd5c631 sickle.xml --- a/sickle.xml Mon Jan 23 06:07:05 2017 -0500 +++ b/sickle.xml Thu Apr 13 16:06:10 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="sickle" name="Sickle" version="1.33">\n+<tool id="sickle" name="Sickle" version="1.33.1" profile="17.01">\n <description>windowed adaptive trimming of FASTQ data</description>\n <requirements>\n <requirement type="package" version="1.33">sickle</requirement>\n@@ -6,60 +6,106 @@\n <requirement type="package" version="1.33">sickle-trim</requirement>\n </requirements>\n <version_command>sickle --version | head -n 1</version_command>\n- <command>\n+ <command><![CDATA[\n+ ## Link in the input files, which also determines the type of the output\n+ #set compressed = ""\n+ #if str($readtype.single_or_paired) == "se":\n+ #if $readtype.input_single.is_of_type(\'fastq.gz\'):\n+ #set read1 = "input_1.fastq.gz"\n+ #set compressed = "-g"\n+ #else\n+ #set read1 = "input_1.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_single}\' ${read1} &&\n+ #else if str($readtype.single_or_paired) == "pe_combo":\n+ #if $readtype.input_combo.is_of_type(\'fastq.gz\'):\n+ #set read1 = "input_1.fastq.gz"\n+ #set compressed = "-g"\n+ #else\n+ #set read1 = "input_1.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_combo}\' ${read1} &&\n+ #else if str($readtype.single_or_paired) == "pe_sep":\n+ #if $readtype.input_paired1.is_of_type(\'fastq.gz\'):\n+ #set read1 = "input_1.fastq.gz"\n+ #set compressed = "-g"\n+ #else\n+ #set read1 = "input_1.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_paired1}\' ${read1} &&\n+\n+ #if $readtype.input_paired2.is_of_type(\'fastq.gz\'):\n+ #set read2 = "input_2.fastq.gz"\n+ #else\n+ #set read2 = "input_2.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_paired2}\' ${read2} &&\n+ #else\n+ #if $readtype.input_paired.forward.is_of_type(\'fastq.gz\'):\n+ #set read1 = "input_1.fastq.gz"\n+ #set compressed = "-g"\n+ #else\n+ #set read1 = "input_1.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_paired.forward}\' ${read1} &&\n+\n+ #if $readtype.input_paired.reverse.is_of_type(\'fastq.gz\'):\n+ #set read2 = "input_2.fastq.gz"\n+ #else\n+ #set read2 = "input_2.fastq"\n+ #end if\n+ ln -f -s \'${readtype.input_paired.reverse}\' ${read2} &&\n+ #end if\n+\n sickle\n \n #if str($readtype.single_or_paired) == "se":\n- se -f "${readtype.input_single}" -o "$output_single"\n+ se -f ${read1} -o \'${output_single}\'\n+\n+ #if $readtype.input_single.is_of_type(\'fastqillumina\', \'fastqillumina.gz\'):\n+ -t illumina\n+ #else if $readtype.input_single.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n+ -t solexa\n+ #else:\n+ -t sanger\n+ #end if\n+ #else if str($readtype.single_or_paired) == "pe_combo":\n+ #if $readtype.output_n:\n+ pe -c ${read1} -M \'${output_combo}\'\n+ #else\n+ pe -c ${read1} -m \'${output_combo}\' -s \'${output_combo_single}\'\n+ #end if\n \n- #if $readtype.input_single.is_of_type(\'fastqillumina\'):\n+ #if $readtype.input_combo.is_of_type(\'fastqillumina\', \'fastqillumina.gz\'):\n+ -t illumina\n+ #else if $readtype.input_combo.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n+ -t solexa\n+ #else:\n+ -t sanger\n+ #end if\n+ #else if str($readtype.single_or_paired) == "pe_sep":\n+ pe -f ${read1} -r ${read2} -o \'${output_paired1}\' -p \'${output_paired2}\' -s \'${output_paired_single}\'\n+\n+ #if $readtype.input_paired1.is_of_type(\'fastqillumina\','..b' />\n- <param name="input_paired1" ftype="fastqsanger" value="test.f.fastq" />\n- <param name="input_paired2" ftype="fastqsanger" value="test.r.fastq" />\n- <param name="qual_threshold" value="34" />\n- <output name="output_paired1" ftype="fastqsanger" file="output.f.fastq" />\n- <output name="output_paired2" ftype="fastqsanger" file="output.r.fastq" />\n- <output name="output_paired_single" ftype="fastqsanger" file="output.s.fastq" />\n+ <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" />\n+ <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" />\n+ <param name="qual_threshold" value="3" />\n+ <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" />\n+ <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" />\n+ <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" />\n+ </test>\n+ <test> <!-- as above, but gzipped -->\n+ <param name="single_or_paired" value="pe_sep" />\n+ <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" />\n+ <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" />\n+ <param name="qual_threshold" value="3" />\n+ <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" />\n+ <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" />\n+ <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />\n </test>\n <test>\n <param name="single_or_paired" value="pe_collection" />\n <param name="input_paired">\n <collection type="paired">\n- <element name="forward" ftype="fastqsanger" value="test.f.fastq" />\n- <element name="reverse" ftype="fastqsanger" value="test.r.fastq" />\n+ <element name="forward" ftype="fastqillumina" value="test.f.fastq" />\n+ <element name="reverse" ftype="fastqillumina" value="test.r.fastq" />\n </collection>\n </param>\n- <param name="qual_threshold" value="34" />\n+ <param name="qual_threshold" value="3" />\n <output_collection name="output_paired_coll" type="paired">\n- <element name="forward" ftype="fastqsanger" file="output.f.fastq" />\n- <element name="reverse" ftype="fastqsanger" file="output.r.fastq" />\n+ <element name="forward" ftype="fastqillumina" file="output.f.fastq" />\n+ <element name="reverse" ftype="fastqillumina" file="output.r.fastq" />\n </output_collection>\n- <output name="output_paired_coll_single" ftype="fastqsanger" file="output.s.fastq" />\n+ <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" />\n+ </test>\n+\n+ <test> <!-- as above, but gzipped -->\n+ <param name="single_or_paired" value="pe_collection" />\n+ <param name="input_paired">\n+ <collection type="paired">\n+ <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" />\n+ <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" />\n+ </collection>\n+ </param>\n+ <param name="qual_threshold" value="3" />\n+ <output_collection name="output_paired_coll" type="paired">\n+ <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" />\n+ <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" />\n+ </output_collection>\n+ <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />\n </test>\n </tests>\n <help>\n' |
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| diff -r edaa8572219d -r 3905ccd5c631 test-data/output.c2.fastq --- 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 |
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| @@ -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 + |
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