| Previous 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 c0d7c69151c3efd66904d47757bdb6ab34c2b39b |
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modified:
sickle.xml |
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added:
test-data/sickle.log |
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| diff -r 6756c87dc2d4 -r 9108bd9450cb sickle.xml --- a/sickle.xml Thu Sep 05 13:14:23 2019 -0400 +++ b/sickle.xml Tue Feb 11 11:01:38 2025 +0000 |
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| b'@@ -1,5 +1,8 @@\n-<tool id="sickle" name="Sickle" version="1.33.2" profile="17.01">\n- <description>windowed adaptive trimming of FASTQ data</description>\n+<tool id="sickle" name="Sickle" version="1.33.3" profile="23.2" license="MIT">\n+ <description>Windowed adaptive trimming of FASTQ data</description>\n+ <xrefs>\n+ <xref type="bio.tools">sickle</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="1.33">sickle-trim</requirement>\n </requirements>\n@@ -120,6 +123,10 @@\n #if $trunc_n:\n -n\n #end if\n+\n+#if $log_out\n+ 2>&1 | tee \'${log}\'\n+#end if\n ]]></command>\n \n <inputs>\n@@ -132,30 +139,29 @@\n </param>\n \n <when value="se">\n- <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />\n+ <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)"/>\n </when>\n \n <when value="pe_combo">\n- <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />\n+ <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)"/>\n <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."/>\n </when>\n \n <when value="pe_sep">\n- <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />\n- <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />\n+ <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)"/>\n+ <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)"/>\n </when>\n \n <when value="pe_collection">\n- <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />\n+ <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection"/>\n </when>\n </conditional>\n \n- <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />\n-\n- <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" />\n-\n- <param name="no_five_prime" type="boolean" label="Don\'t do 5\' trimming" help="(-x)" />\n- <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)" />\n+ <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)"/>\n+ <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)"/>\n+ <param name="no_five_prime" type="boolean" label="Don\'t do 5\' trimming" help="(-x)"/>\n+ <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)"/>\n+ <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>\n </inputs>\n \n <outputs>\n@@ -187,76 +193,90 @@\n <filter>readtype['..b'type="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+ <test expect_num_outputs="4">\n+ <param name="single_or_paired" value="pe_collection"/>\n <param name="input_paired">\n <collection type="paired">\n- <element name="forward" ftype="fastqillumina" value="test.f.fastq" />\n- <element name="reverse" ftype="fastqillumina" 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="3" />\n+ <param name="qual_threshold" value="3"/>\n <output_collection name="output_paired_coll" type="paired">\n- <element name="forward" ftype="fastqillumina" file="output.f.fastq" />\n- <element name="reverse" ftype="fastqillumina" 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="fastqillumina" 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+ <test expect_num_outputs="4"> <!-- 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+ <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+ <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+ <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+ <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="single_or_paired" value="pe_combo"/>\n+ <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>\n+ <param name="qual_threshold" value="3"/>\n+ <param name="log_out" value="yes"/>\n+ <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq"/>\n+ <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq"/>\n+ <output name="log" file="sickle.log" ftype="txt"/>\n </test>\n </tests>\n <help>\n+\n **What it does**\n \n Most modern sequencing technologies produce reads that have\n' |
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| diff -r 6756c87dc2d4 -r 9108bd9450cb test-data/sickle.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sickle.log Tue Feb 11 11:01:38 2025 +0000 |
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| @@ -0,0 +1,6 @@ + +FastQ paired records kept: 2484 (1242 pairs) +FastQ single records kept: 8 +FastQ paired records discarded: 0 (0 pairs) +FastQ single records discarded: 8 + |