Mercurial > repos > iuc > prinseq
changeset 2:74afc47f326c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
| author | iuc |
|---|---|
| date | Fri, 03 Mar 2017 14:58:49 -0500 |
| parents | 6b865dde1baa |
| children | 02befcb391f5 |
| files | prinseq.xml tool_dependencies.xml |
| diffstat | 2 files changed, 29 insertions(+), 80 deletions(-) [+] |
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--- a/prinseq.xml Sat Jan 21 06:27:29 2017 -0500 +++ b/prinseq.xml Fri Mar 03 14:58:49 2017 -0500 @@ -1,10 +1,6 @@ -<tool id="prinseq" name="PRINSEQ" version="0.1.0"> +<tool id="prinseq" name="PRINSEQ" version="0.20.4"> <description>to process quality of sequences</description> - <requirements> - <requirement type="package" version="5.18.1">perl</requirement> - <!--<requirement type="package" version="2.90">perl-json</requirement> - <requirement type="package" version="1.106">perl-cairo</requirement>--> <requirement type="package" version="0.20.4">prinseq</requirement> </requirements> @@ -34,13 +30,13 @@ prinseq-lite.pl #if $seq_type.seq_type_opt == "single": - -fastq "$seq_type.input_singles" + -fastq '$seq_type.input_singles' #if $seq_type.input_singles.is_of_type('fastqillumina'): -phred64 #end if #else: - -fastq "$seq_type.input_mate1" - -fastq2 "$seq_type.input_mate2" + -fastq '$seq_type.input_mate1' + -fastq2 '$seq_type.input_mate2' #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext: #import sys #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' ) @@ -69,7 +65,7 @@ #set quality_filter_treatments=$filter_treatments.quality_filter_treatments #if $quality_filter_treatments.apply_quality_filter_treatments == "true": - #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments + #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments #if $min_quality_filter_treatments.apply_min_quality_filter_treatments == "true": -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value #end if @@ -211,18 +207,17 @@ -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments #end if - #end if + #end if #* -graph_stats "$graph_stats" -graph_data tmp/stats.gd - - && + && prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html *# -]]> +]]> </command> <inputs> @@ -261,7 +256,7 @@ <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)"/> </when> <when value="false" /> - </conditional> + </conditional> <conditional name="max_length_filter_treatments"> <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."> <option value="true">Yes</option> @@ -271,10 +266,10 @@ <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)"/> </when> <when value="false" /> - </conditional> + </conditional> </when> <when value="false" /> - </conditional> + </conditional> <conditional name="quality_filter_treatments"> <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."> <option value="true" selected="true">Yes</option> @@ -312,7 +307,7 @@ <option value="true" selected="true">Yes</option> <option value="false">No</option> </param> - <when value="true"> + <when value="true"> <param name="min_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="15" label="Minimum mean score threshold to conserve sequences" help="(-min_qual_mean)"/> </when> <when value="false" /> @@ -322,7 +317,7 @@ <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> - <when value="true"> + <when value="true"> <param name="max_mean_quality_filter_treatment_value" type="integer" min="0" max="40" value="40" label="Maximum mean score threshold to conserve sequences" help="(-max_qual_mean)"/> </when> <when value="false" /> @@ -401,14 +396,14 @@ <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help="(-lc_method)"> <option value="dust">Dust</option> <option value="entropy" >Entropy</option> - </param> + </param> <param name="threshold_complexity_filter_treatments" type="integer" min="0" max="100" value="2" label="Threshold value used to filter sequences by sequence complexity" help="The dust method uses the threshold as maximum allowed score and the entropy method as minimum allowed value.(-lc_threshold)"/> </when> <when value="false" /> </conditional> </when> <when value="false" /> - </conditional> + </conditional> <conditional name="trimming_treatments"> <param name="apply_trimming_treatments" type="select" label="Apply trimming treatments?" help=""> @@ -622,50 +617,41 @@ </inputs> <outputs> - <data format="fastq" name="good_sequence_file" - from_work_dir="tmp/good_sequences.fastq" + <data format="fastq" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq" label="${tool.name} on ${on_string}: Good sequences" > <filter>seq_type['seq_type_opt'] == "single"</filter> </data> - <data format="fastq" name="rejected_sequence_file" - from_work_dir="tmp/rejected_sequences.fastq" + <data format="fastq" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq" label="${tool.name} on ${on_string}: Rejected sequences" > <filter>seq_type['seq_type_opt'] == "single"</filter> </data> - <data format="fastq" name="good_sequences_1_file" - from_work_dir="tmp/good_sequences_1.fastq" + <data format="fastq" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq" label="${tool.name} on ${on_string}: Good sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <data format="fastq" name="good_sequences_1_singletons_file" - from_work_dir="tmp/good_sequences_1_singletons.fastq" + <data format="fastq" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq" label="${tool.name} on ${on_string}: Good singleton sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <data format="fastq" name="rejected_sequence_1_file" - from_work_dir="tmp/rejected_sequences_1.fastq" + <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq" label="${tool.name} on ${on_string}: Rejected sequences for R1" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <data format="fastq" name="good_sequences_2_file" - from_work_dir="tmp/good_sequences_2.fastq" + <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq" label="${tool.name} on ${on_string}: Good sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <data format="fastq" name="good_sequences_2_singletons_file" - from_work_dir="tmp/good_sequences_2_singletons.fastq" + <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq" label="${tool.name} on ${on_string}: Good singleton sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <data format="fastq" name="rejected_sequence_2_file" - from_work_dir="tmp/rejected_sequences_2.fastq" + <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq" label="${tool.name} on ${on_string}: Rejected sequences for R2" > <filter>seq_type['seq_type_opt'] == "paired"</filter> </data> - <!--<data format="html" name="html_file" - from_work_dir="stats_html.html" + <!--<data format="html" name="html_file" from_work_dir="stats_html.html" label="${tool.name} on ${on_string}: Summary" />--> </outputs> @@ -674,8 +660,8 @@ <param name='seq_type_opt' value="single"/> <param name="input_singles" value="prinseq_input_sequences.fastq"/> <param name='apply_filter_treatments' value="true"/> - <param name='apply_length_filter_treatments' value="true"/> - <param name='apply_min_length_filter_treatments' value="true"/> + <param name='apply_length_filter_treatments' value="true"/> + <param name='apply_min_length_filter_treatments' value="true"/> <param name="min_length_filter_treatment_value" value="60"/> <param name='apply_max_length_filter_treatments' value="false" /> <param name='apply_quality_filter_treatments' value="true"/> @@ -688,7 +674,7 @@ <param name='apply_base_content_filter_treatments' value="true"/> <param name='apply_GC_perc_content_filter_treatments' value="false"/> <param name='apply_N_number_content_filter_treatments' value="false"/> - <param name='apply_N_percentage_content_filter_treatments' value="true"/> + <param name='apply_N_percentage_content_filter_treatments' value="true"/> <param name="N_percentage_content_filter_treatment_value" value="2"/> <param name='apply_other_base_content_filter_treatments' value="false"/> <param name='apply_complexity_filter_treatments' value="false"/> @@ -710,11 +696,10 @@ </tests> <help><![CDATA[ - **What it does** PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets. -This tool allow to process the sequences with filtering and trimming. +This tool allow to process the sequences with filtering and trimming. More information on `PRINSEQ manual <http://prinseq.sourceforge.net/manual.html>`_. ----- @@ -736,7 +721,7 @@ Several filter treatments are proposed: - - Filters based on sequence length + - Filters based on sequence length - Filters based on quality score - Filters based on base content @@ -754,7 +739,6 @@ The output file is a sequence file with sequences and quality from input file which have undergone filter and trimming. - ]]> </help>
--- a/tool_dependencies.xml Sat Jan 21 06:27:29 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>