| Previous changeset 7:18d17a5bfe11 (2017-10-15) Next changeset 9:e3ad639c692a (2017-12-01) |
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Commit message:
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit aa6136c5fa32b987f64bd2b0dc1f72018038b0bb |
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modified:
porechop.xml |
| b |
| diff -r 18d17a5bfe11 -r 852b3fe95c20 porechop.xml --- a/porechop.xml Sun Oct 15 17:32:40 2017 -0400 +++ b/porechop.xml Fri Oct 20 23:11:21 2017 -0400 |
| b |
| b'@@ -50,28 +50,25 @@\n \n ##--Adapter Trim Options--------------------------\n \n- #if str($trim_section.trim_options.trim) == "yes":\n+ #if str($trim_section.trim) == "no":\n+ --untrimmed\n+ #end if\n \n- --adapter_threshold $trim_section.trim_options.adapter_threshold\n- --check_reads $trim_section.trim_options.check_reads\n- --scoring_scheme $trim_section.trim_options.scoring_scheme\n-\n- --end_size $trim_section.trim_options.end_size\n- --end_threshold $trim_section.trim_options.end_threshold\n- --min_trim_size $trim_section.trim_options.min_trim_size\n- --extra_end_trim $trim_section.trim_options.extra_end_trim\n+ --adapter_threshold $adapter_section.adapter_threshold\n+ --check_reads $adapter_section.check_reads\n+ --scoring_scheme $adapter_section.scoring_scheme\n \n- $trim_section.trim_options.discard_middle\n- --middle_threshold $trim_section.trim_options.middle_threshold\n- --extra_middle_trim_good_side $trim_section.trim_options.extra_middle_trim_good_side\n- --extra_middle_trim_bad_side $trim_section.trim_options.extra_middle_trim_bad_side\n- --min_split_read_size $trim_section.trim_options.min_split_read_size\n+ --end_size $adapter_section.end_size\n+ --end_threshold $adapter_section.end_threshold\n+ --min_trim_size $adapter_section.min_trim_size\n+ --extra_end_trim $adapter_section.extra_end_trim\n \n+ $adapter_section.discard_middle\n+ --middle_threshold $adapter_section.middle_threshold\n+ --extra_middle_trim_good_side $adapter_section.extra_middle_trim_good_side\n+ --extra_middle_trim_bad_side $adapter_section.extra_middle_trim_bad_side\n+ --min_split_read_size $adapter_section.min_split_read_size\n \n- #else:\n- --untrimmed\n-\n- #end if\n \n | perl $__tool_directory__/porechop_summarize.pl\n > $result_table\n@@ -107,29 +104,25 @@\n </section>\n \n <section name="trim_section" title="Trimming Options" expanded="True">\n- <conditional name="trim_options">\n <param name="trim" type="select" label="Perform adapter trimming" help="">\n <option value="no" selected="true">no</option>\n <option value="yes">yes</option>\n </param>\n- <when value="no" />\n- <when value="yes">\n- <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />\n- <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />\n- <param argument="--barcode_diff" size="4" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />\n- <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" />\n- <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" />\n- <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" />\n- <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " />\n- <param argument="--end_threshold" size="4" type="float" value="75.0" min="0" max="100" label="End adapter trim threshold identity" />\n+ </section>\n+ <section name="adapter_section" title="Adapter Options" expanded="False">\n+ <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />\n+ <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />\n+ <par'..b'_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />\n- </when>\n- </conditional>\n+ <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" />\n+ <param argument="--middle_threshold" size="4" type="float" value="85.0" min="0" max="100" label="Middle adapter trim threshold identity" />\n+ <param argument="--extra_middle_trim_good_side" size="4" type="integer" value="10" label="Adjacent bases to trim on good side" />\n+ <param argument="--extra_middle_trim_bad_side" size="4" type="integer" value="100" label="Adjacent bases to trim on bad side" />\n+ <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />\n </section>\n \n </inputs>\n@@ -157,10 +150,10 @@\n <param name="input" value="test_barcodes.fastq" ftype="fastq" />\n <param name="demux" value="yes" />\n <output_collection name="output_collection_fastq" type="list" count="4">\n- <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/>\n- <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/>\n- <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/>\n- <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/>\n+ <element name="BC01" file="bar1/BC01.fastq" compare="diff" decompress="true"/>\n+ <element name="BC02" file="bar1/BC02.fastq" compare="diff" decompress="true"/>\n+ <element name="BC03" file="bar1/BC03.fastq" compare="diff" decompress="true"/>\n+ <element name="none" file="bar1/none.fastq" compare="diff" decompress="true"/>\n </output_collection>\n </test>\n <test>\n@@ -168,10 +161,10 @@\n <param name="demux" value="yes" />\n <param name="require_two_barcodes" value="True" />\n <output_collection name="output_collection_fastq" type="list" count="4">\n- <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/>\n- <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/>\n- <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/>\n- <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/>\n+ <element name="BC01" file="bar2/BC01.fastq" compare="diff" decompress="true"/>\n+ <element name="BC02" file="bar2/BC02.fastq" compare="diff" decompress="true"/>\n+ <element name="BC03" file="bar2/BC03.fastq" compare="diff" decompress="true"/>\n+ <element name="none" file="bar2/none.fastq" compare="diff" decompress="true"/>\n </output_collection>\n </test>\n <test>\n@@ -180,9 +173,9 @@\n <param name="trim" value="yes" />\n <param name="discard_unassigned" value="yes" />\n <output_collection name="output_collection_fastq" type="list" count="3">\n- <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>\n- <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>\n- <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>\n+ <element name="BC01" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>\n+ <element name="BC02" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>\n+ <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>\n </output_collection>\n </test>\n </tests>\n' |