| Previous changeset 5:3905ccd5c631 (2017-04-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" |
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modified:
sickle.xml |
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removed:
tool_dependencies.xml |
| b |
| diff -r 3905ccd5c631 -r 6756c87dc2d4 sickle.xml --- a/sickle.xml Thu Apr 13 16:06:10 2017 -0400 +++ b/sickle.xml Thu Sep 05 13:14:23 2019 -0400 |
| [ |
| b'@@ -1,129 +1,126 @@\n-<tool id="sickle" name="Sickle" version="1.33.1" profile="17.01">\n+<tool id="sickle" name="Sickle" version="1.33.2" profile="17.01">\n <description>windowed adaptive trimming of FASTQ data</description>\n <requirements>\n- <requirement type="package" version="1.33">sickle</requirement>\n- <!-- conda dependency -->\n <requirement type="package" version="1.33">sickle-trim</requirement>\n </requirements>\n <version_command>sickle --version | head -n 1</version_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}\' ${read1} &&\n+## Link in the input files, which also determines the type of the output\n+#set compressed = ""\n+#if str($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+ #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 $readtype.input_paired.reverse.is_of_type(\'fastq.gz\'):\n- #set read2 = "input_2.fastq.gz"\n- #else\n- #set read2 = "input_2.fastq"\n- '..b'($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+ #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_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+ #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\', \'fastqillumina.gz\'):\n- -t illumina\n- #else if $readtype.input_paired1.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n- -t solexa\n- #else:\n- -t sanger\n- #end if\n- #else if str($readtype.single_or_paired) == "pe_collection":\n- pe -f ${read1} -r ${read2} -o \'${output_paired_coll.forward}\' -p \'${output_paired_coll.reverse}\' -s \'${output_paired_coll_single}\'\n+ #if $readtype.input_paired1.is_of_type(\'fastqillumina\', \'fastqillumina.gz\'):\n+ -t illumina\n+ #else if $readtype.input_paired1.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n+ -t solexa\n+ #else:\n+ -t sanger\n+ #end if\n+#else if str($readtype.single_or_paired) == "pe_collection":\n+ pe -f ${read1} -r ${read2} -o \'${output_paired_coll.forward}\' -p \'${output_paired_coll.reverse}\' -s \'${output_paired_coll_single}\'\n \n- #if $readtype.input_paired.forward.is_of_type(\'fastqillumina\', \'fastqillumina.gz\'):\n- -t illumina\n- #else if $readtype.input_paired.forward.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n- -t solexa\n- #else:\n- -t sanger\n- #end if\n- #end if\n+ #if $readtype.input_paired.forward.is_of_type(\'fastqillumina\', \'fastqillumina.gz\'):\n+ -t illumina\n+ #else if $readtype.input_paired.forward.is_of_type(\'fastqsolexa\', \'fastqsolexa.gz\'):\n+ -t solexa\n+ #else:\n+ -t sanger\n+ #end if\n+#end if\n \n- $compressed\n+$compressed\n \n- #if str($qual_threshold) != "":\n- -q $qual_threshold\n- #end if\n-\n- #if str($length_threshold) != "":\n- -l $length_threshold\n- #end if\n+#if str($qual_threshold) != "":\n+ -q $qual_threshold\n+#end if\n \n- #if $no_five_prime:\n- -x\n- #end if\n+#if str($length_threshold) != "":\n+ -l $length_threshold\n+#end if\n \n- #if $trunc_n:\n- -n\n- #end if\n- ]]>\n- </command>\n+#if $no_five_prime:\n+ -x\n+#end if\n+\n+#if $trunc_n:\n+ -n\n+#end if\n+ ]]></command>\n \n <inputs>\n <conditional name="readtype">\n@@ -350,8 +347,6 @@\n \n Copyright: Nikhil Joshi\n \n-http://bioinformatics.ucdavis.edu\n-\n http://github.com/najoshi/sickle\n </help>\n <citations>\n' |
| b |
| diff -r 3905ccd5c631 -r 6756c87dc2d4 tool_dependencies.xml --- a/tool_dependencies.xml Thu Apr 13 16:06:10 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="zlib" version="1.2.8"> - <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="sickle" version="1.33"> - <install version="1.0"> - <actions> - <action target_filename="sickle-1.33.tar.gz" type="download_by_url">https://github.com/najoshi/sickle/archive/v1.33.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="411985b46ae8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="zlib" version="1.2.8" /> - </repository> - </action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>sickle</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Sickle is a windowed adaptive trimming tool for FASTQ files using quality. - </readme> - </package> -</tool_dependency> |