| Previous changeset 1:6b865dde1baa (2017-01-21) Next changeset 3:02befcb391f5 (2017-05-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b |
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modified:
prinseq.xml |
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removed:
tool_dependencies.xml |
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| diff -r 6b865dde1baa -r 74afc47f326c prinseq.xml --- a/prinseq.xml Sat Jan 21 06:27:29 2017 -0500 +++ b/prinseq.xml Fri Mar 03 14:58:49 2017 -0500 |
| [ |
| b'@@ -1,10 +1,6 @@\n-<tool id="prinseq" name="PRINSEQ" version="0.1.0">\n+<tool id="prinseq" name="PRINSEQ" version="0.20.4">\n <description>to process quality of sequences</description>\n- \n <requirements>\n- <requirement type="package" version="5.18.1">perl</requirement>\n- <!--<requirement type="package" version="2.90">perl-json</requirement>\n- <requirement type="package" version="1.106">perl-cairo</requirement>-->\n <requirement type="package" version="0.20.4">prinseq</requirement>\n </requirements>\n \n@@ -34,13 +30,13 @@\n \n prinseq-lite.pl\n #if $seq_type.seq_type_opt == "single":\n- -fastq "$seq_type.input_singles"\n+ -fastq \'$seq_type.input_singles\'\n #if $seq_type.input_singles.is_of_type(\'fastqillumina\'):\n -phred64\n #end if\n #else:\n- -fastq "$seq_type.input_mate1"\n- -fastq2 "$seq_type.input_mate2"\n+ -fastq \'$seq_type.input_mate1\'\n+ -fastq2 \'$seq_type.input_mate2\'\n #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:\n #import sys\n #silent sys.stderr.write( \'Both pairs from your paired-end library need to be from the same filetype.\' )\n@@ -69,7 +65,7 @@\n \n #set quality_filter_treatments=$filter_treatments.quality_filter_treatments\n #if $quality_filter_treatments.apply_quality_filter_treatments == "true":\n- #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments \n+ #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments\n #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true":\n -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value\n #end if\n@@ -211,18 +207,17 @@\n -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments\n #end if\n \n- #end if \n+ #end if\n \n #*\n -graph_stats "$graph_stats"\n -graph_data tmp/stats.gd\n \n- \n- && \n+ &&\n \n prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html\n *#\n-]]> \n+]]>\n </command>\n \n <inputs>\n@@ -261,7 +256,7 @@\n <param name="min_length_filter_treatment_value" type="integer" min="0" max="3000" value="60" label="Minimum length threshold to conserve sequences" help="(-min_len)"/>\n </when>\n <when value="false" />\n- </conditional> \n+ </conditional>\n <conditional name="max_length_filter_treatments">\n <param name="apply_max_length_filter_treatments" type="select" label="Filter too big sequences?" help="By default, no treatment based on a maximal length is made.">\n <option value="true">Yes</option>\n@@ -271,10 +266,10 @@\n <param name="max_length_filter_treatment_value" type="integer" min="0" max="3000" value="1000" label="Maximal length threshold to conserve sequences" help="(-max_len)"/>\n </when>\n <when value="false" />\n- </conditional> \n+ </conditional>\n </when>\n <when value="false" />\n- </conditional> \n+ </conditional>\n <conditional name="quality_filter_treatments">\n <param name="apply_quality_filter_treatments" type="select" label="Filter sequences based on quality score?" help="By default, sequences with a mean score below 15 are removed.">\n '..b' <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"\n label="${tool.name} on ${on_string}: Rejected sequences for R1" >\n <filter>seq_type[\'seq_type_opt\'] == "paired"</filter>\n </data>\n- <data format="fastq" name="good_sequences_2_file" \n- from_work_dir="tmp/good_sequences_2.fastq"\n+ <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"\n label="${tool.name} on ${on_string}: Good sequences for R2" >\n <filter>seq_type[\'seq_type_opt\'] == "paired"</filter>\n </data>\n- <data format="fastq" name="good_sequences_2_singletons_file" \n- from_work_dir="tmp/good_sequences_2_singletons.fastq"\n+ <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"\n label="${tool.name} on ${on_string}: Good singleton sequences for R2" >\n <filter>seq_type[\'seq_type_opt\'] == "paired"</filter>\n </data>\n- <data format="fastq" name="rejected_sequence_2_file" \n- from_work_dir="tmp/rejected_sequences_2.fastq"\n+ <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"\n label="${tool.name} on ${on_string}: Rejected sequences for R2" >\n <filter>seq_type[\'seq_type_opt\'] == "paired"</filter>\n </data>\n \n- <!--<data format="html" name="html_file" \n- from_work_dir="stats_html.html"\n+ <!--<data format="html" name="html_file" from_work_dir="stats_html.html"\n label="${tool.name} on ${on_string}: Summary" />-->\n </outputs>\n \n@@ -674,8 +660,8 @@\n <param name=\'seq_type_opt\' value="single"/>\n <param name="input_singles" value="prinseq_input_sequences.fastq"/>\n <param name=\'apply_filter_treatments\' value="true"/>\n- <param name=\'apply_length_filter_treatments\' value="true"/> \n- <param name=\'apply_min_length_filter_treatments\' value="true"/> \n+ <param name=\'apply_length_filter_treatments\' value="true"/>\n+ <param name=\'apply_min_length_filter_treatments\' value="true"/>\n <param name="min_length_filter_treatment_value" value="60"/>\n <param name=\'apply_max_length_filter_treatments\' value="false" />\n <param name=\'apply_quality_filter_treatments\' value="true"/>\n@@ -688,7 +674,7 @@\n <param name=\'apply_base_content_filter_treatments\' value="true"/>\n <param name=\'apply_GC_perc_content_filter_treatments\' value="false"/>\n <param name=\'apply_N_number_content_filter_treatments\' value="false"/>\n- <param name=\'apply_N_percentage_content_filter_treatments\' value="true"/> \n+ <param name=\'apply_N_percentage_content_filter_treatments\' value="true"/>\n <param name="N_percentage_content_filter_treatment_value" value="2"/>\n <param name=\'apply_other_base_content_filter_treatments\' value="false"/>\n <param name=\'apply_complexity_filter_treatments\' value="false"/>\n@@ -710,11 +696,10 @@\n </tests>\n \n <help><![CDATA[\n-\n **What it does**\n \n PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets.\n-This tool allow to process the sequences with filtering and trimming. \n+This tool allow to process the sequences with filtering and trimming.\n More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_.\n \n -----\n@@ -736,7 +721,7 @@\n \n Several filter treatments are proposed:\n \n- - Filters based on sequence length \n+ - Filters based on sequence length\n - Filters based on quality score\n - Filters based on base content\n \n@@ -754,7 +739,6 @@\n \n The output file is a sequence file with sequences and quality from input file\n which have undergone filter and trimming.\n-\n ]]>\n </help>\n \n' |
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| diff -r 6b865dde1baa -r 74afc47f326c tool_dependencies.xml --- a/tool_dependencies.xml Sat Jan 21 06:27:29 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,35 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <!--<package name="perl-json" version="2.90"> - <repository name="package_perl_json_2_90" owner="iuc" prior_installation_required="True" /> - </package> - <package name="perl-cairo" version="1.106"> - <repository name="package_perl_cairo_1_106" owner="iuc" prior_installation_required="True" /> - </package>--> - <package name="prinseq" version="0.20.4"> - <install version="1.0"> - <actions> - <action sha256sum="9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f" type="download_by_url">http://downloads.sourceforge.net/project/prinseq/standalone/prinseq-lite-0.20.4.tar.gz</action> - <action type="move_file"> - <source>prinseq-lite.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="chmod"><file mode="755">$INSTALL_DIR/prinseq-lite.pl</file></action> - - <action type="move_file"> - <source>prinseq-graphs-noPCA.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="chmod"><file mode="755">$INSTALL_DIR/prinseq-graphs-noPCA.pl</file></action> - - <action type="set_environment"> - <environment_variable action="set_to" name="PRINSEQ_DIR">$INSTALL_DIR/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency> |