Mercurial > repos > bebatut > prinseq
diff prinseq.xml @ 2:6912790a4287 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit c9e8b7a0212c9fdc3b91ca0c38129a2a05e4abe2-dirty
| author | bebatut |
|---|---|
| date | Tue, 10 Nov 2015 09:23:59 -0500 |
| parents | 65f03479b3ba |
| children | 10ac5c567b73 |
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--- a/prinseq.xml Tue Oct 27 13:11:28 2015 -0400 +++ b/prinseq.xml Tue Nov 10 09:23:59 2015 -0500 @@ -1,6 +1,6 @@ <tool id="prinseq" name="PRINSEQ" version="0.1.0"> <description>to process quality of sequences</description> - + <requirements> <requirement type="package" version="0.20.4">prinseq</requirement> </requirements> @@ -17,22 +17,29 @@ description="" /> </stdio> - <command><![CDATA[ - perl prinseq-lite.pl - -fastq $input_sequence_file - -out_good stdout - -out_bad null + <version_command> +<![CDATA[ + perl \${PRINSEQ_DIR}/prinseq-lite.pl --version +]]> + </version_command> + + <command> +<![CDATA[ + perl \${PRINSEQ_DIR}/prinseq-lite.pl + -fastq $sequence_to_control_file + -out_good good_sequences + -out_bad rejected_sequences #if $filter_treatments.apply_filter_treatments : #set length_filter_treatments=$filter_treatments.length_filter_treatments #if $length_filter_treatments.apply_length_filter_treatments : #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments #if $min_length_filter_treatments.apply_min_length_filter_treatments : - -min_len $min_length_filter_treatments.value + -min_len $min_length_filter_treatments.min_length_filter_treatment_value #end if #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments #if $max_length_filter_treatments.apply_max_length_filter_treatments : - -max_len $min_length_filter_treatments.value + -max_len $max_length_filter_treatments.max_length_filter_treatment_value #end if #end if @@ -40,21 +47,21 @@ #if $quality_filter_treatments.apply_quality_filter_treatments: #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments #if $min_quality_filter_treatments.apply_min_quality_filter_treatments : - -min_qual_score $min_quality_filter_treatments.value + -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value #end if #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments #if $max_quality_filter_treatments.apply_max_quality_filter_treatments : - -max_qual_score $max_quality_filter_treatments.value + -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value #end if #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments: #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments: - -min_qual_mean $min_mean_quality_filter_treatments.value + -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value #end if #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments: - -max_qual_mean $max_mean_quality_filter_treatments.value + -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value #end if #end if #end if @@ -65,20 +72,20 @@ #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments : #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments : - -min_gc $min_GC_perc_content_filter_treatments.value + -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value #end if set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments : - -max_gc $max_GC_perc_content_filter_treatments.value + -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value #end if #end if #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments : - -ns_max_n $N_number_content_filter_treatments.value + -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value #end if #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments : - -ns_max_p $N_percentage_content_filter_treatments.value + -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value #end if #if $base_content_filter_treatments.apply_other_base_content_filter_treatments : -noniupac @@ -96,7 +103,7 @@ #if $trimming_treatments.apply_trimming_treatments : #set length_trimming_treatments=$trimming_treatments.length_trimming_treatments #if $length_trimming_treatments.apply_length_trimming_treatments : - -trim_to_len $length_trimming_treatments.value + -trim_to_len $length_trimming_treatments.length_trimming_treatment_value #end if #set position_trimming_treatments=$trimming_treatments.position_trimming_treatments @@ -105,22 +112,22 @@ #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments : #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments #if $left_position_trimming_treatments.apply_left_position_trimming_treatments : - -trim_left $left_position_trimming_treatments.value + -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value #end if #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments #if $right_position_trimming_treatments.apply_right_position_trimming_treatments : - -trim_right $right_position_trimming_treatments.value + -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value #end if #end if #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments : #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments : - -trim_left_p $left_percentage_position_trimming_treatments.value + -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value #end if #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments : - -trim_right_p $right_percentage_position_trimming_treatments.value + -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value #end if #end if #end if @@ -131,22 +138,22 @@ #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments : #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments : - -trim_tail_left $left_a_t_tail_trimming_treatments.value + -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value #end if #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments #if right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments : - -trim_tail_right $right_a_t_tail_trimming_treatments.value + -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value #end if #end if #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments : #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments : - -trim_ns_left $left_ns_tail_trimming_treatments.value + -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value #end if #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments : - -trim_ns_right $right_ns_tail_trimming_treatments.value + -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value #end if #end if #end if @@ -155,11 +162,11 @@ #if $quality_trimming_treatments.apply_quality_trimming_treatments : #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments : - -trim_qual_left $left_quality_trimming_treatments.value + -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value #end if #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments : - -trim_qual_right $right_quality_trimming_treatments.value + -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value #end if -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments @@ -168,62 +175,108 @@ #end if #end if - - >> $good_sequence_file - ]]> +]]> </command> <inputs> - <param name="input_sequence_file" type="data" format="fastq" label="Input sequence file" help="The file must be in fastq format for quality scores"/> + <param name="sequence_to_control_file" type="data" format="fastq" label="Input + sequence file" help="The file must be in fastq format for quality + scores"/> <conditional name="filter_treatments"> - <param name='apply_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Apply filter treatments?" help=""/> - <when value="yes"> + <param name='apply_filter_treatments' type='boolean' checked="true" + label="Apply filter treatments?" help=""/> + <when value="true"> <conditional name="length_filter_treatments"> - <param name='apply_length_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequence based on their length?" help="By default, sequences smaller than 60 bp are removed. No top threshold is defined"/> - <when value="yes"> + <param name='apply_length_filter_treatments' type='boolean' + checked="true" label="Filter sequence based on their + length?" help="By default, sequences smaller than 60 bp + are removed. No top threshold is defined"/> + <when value="true"> <conditional name="min_length_filter_treatments"> - <param name='apply_min_length_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter too small sequences?" help="By default, sequences smaller than 60 bp are removed."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="60" label="Minimum length threshold to conserve sequences" help=""/> + <param name='apply_min_length_filter_treatments' + type='boolean' checked="true" label="Filter too + small sequences?" help="By default, sequences + smaller than 60 bp are removed."/> + <when value="true"> + <param name="min_length_filter_treatment_value" type="integer" min="0" + max="3000" value="60" label="Minimum length t + hreshold to conserve sequences" help=""/> </when> </conditional> <conditional name="max_length_filter_treatments"> - <param name='apply_max_length_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter too big sequences?" help="By default, no treatment based on a maximal length is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="1000" label="Maximal length threshold to conserve sequences" help=""/> + <param name='apply_max_length_filter_treatments' + type='boolean' checked="false" label="Filter too + big sequences?" help="By default, no treatment + based on a maximal length is made"/> + <when value="true"> + <param name="max_length_filter_treatment_value" type="integer" min="0" + max="3000" value="1000" label="Maximal length + threshold to conserve sequences" help=""/> </when> </conditional> </when> </conditional> <conditional name="quality_filter_treatments"> - <param name='apply_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on quality score?" help="By default, sequences with a mean score below 15 are removed."/> - <when value="yes"> + <param name='apply_quality_filter_treatments' type='boolean' + checked="true" label="Filter sequences based on quality + score?" help="By default, sequences with a mean score + below 15 are removed."/> + <when value="true"> <conditional name="min_quality_filter_treatments"> - <param name='apply_min_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their minimum score?" help="By default, no treatment based on a minimum score is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="2" label="Minimum score threshold to conserve sequences" help=""/> + <param name='apply_min_quality_filter_treatments' + type='boolean' checked="false" label="Filter sequences + based on their minimum score?" help="By default, + no treatment based on a minimum score is made"/> + <when value="true"> + <param name="min_quality_filter_treatment_value" type="integer" min="0" + max="40" value="2" label="Minimum score threshold + to conserve sequences" help=""/> </when> </conditional> <conditional name="max_quality_filter_treatments"> - <param name='apply_max_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their maximum score?" help="By default, no treatment based on a maximum score is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="38" label="Maximum score threshold to conserve sequences" help=""/> + <param name='apply_max_quality_filter_treatments' + type='boolean' checked="false" label="Filter sequences + based on their maximum score?" help="By default, + no treatment based on a maximum score is made"/> + <when value="true"> + <param name="max_quality_filter_treatment_value" type="integer" min="0" + max="40" value="38" label="Maximum score + threshold to conserve sequences" help=""/> </when> </conditional> <conditional name="mean_quality_filter_treatments"> - <param name='apply_mean_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their mean score?" help="By default, sequences with a mean score below 15 are removed."/> - <when value="yes"> + <param name='apply_mean_quality_filter_treatments' + type='boolean' checked="true" label="Filter sequences + based on their mean score?" help="By default, + sequences with a mean score below 15 are removed."/> + <when value="true"> <conditional name="min_mean_quality_filter_treatments"> - <param name='apply_min_mean_quality_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences with too small mean score?" help="By default, sequences with a mean score below 15 are removed."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="15" label="Minimum mean score threshold to conserve sequences" help=""/> + <param name='apply_min_mean_quality_filter_treatments' + type='boolean' checked="true" label="Filter + sequences with too small mean score?" + help="By default, sequences with a mean + score below 15 are removed."/> + <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=""/> </when> </conditional> <conditional name="max_mean_quality_filter_treatments"> - <param name='apply_max_mean_quality_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too high mean score?" help="By default, no treatment based on a maximum mean score is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="40" label="Maximum mean score threshold to conserve sequences" help=""/> + <param name='apply_max_mean_quality_filter_treatments' + type='boolean' checked="false" label="Filter + sequences with too high mean score?" + help="By default, no treatment based on + a maximum mean score is made"/> + <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=""/> </when> </conditional> </when> @@ -231,95 +284,189 @@ </when> </conditional> <conditional name="base_content_filter_treatments"> - <param name='apply_base_content_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their base content?" help="By default, sequences with more than 2% of N bases are removed."/> - <when value="yes"> + <param name='apply_base_content_filter_treatments' + type='boolean' checked="true" label="Filter sequences + based on their base content?" help="By default, sequences + with more than 2% of N bases are removed."/> + <when value="true"> <conditional name="GC_perc_content_filter_treatments"> - <param name='apply_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their GC percentage?" help="By default, no treatment based on GC percentage is made."/> - <when value="yes"> + <param name='apply_GC_perc_content_filter_treatments' + type='boolean' checked="false" label="Filter + sequences based on their GC percentage?" + help="By default, no treatment based on GC percentage + is made."/> + <when value="true"> <conditional name="min_GC_perc_content_filter_treatments"> - <param name='apply_min_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too small GC percentage?" help="By default, no treatment based on GC percentage is made."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="100" value="10" label="Minimal GC percentage threshold to conserve sequences" help=""/> + <param name='apply_min_GC_perc_content_filter_treatments' + type='boolean' checked="false" label="Filter + sequences with too small GC percentage?" + help="By default, no treatment based on + GC percentage is made."/> + <when value="true"> + <param name="min_GC_perc_content_filter_treatment_value" + type="integer" min="0" + max="100" value="10" label="Minimal + GC percentage threshold to conserve + sequences" help=""/> </when> </conditional> <conditional name="max_GC_perc_content_filter_treatments"> - <param name='apply_max_GC_perc_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with too high GC percentage?" help="By default, no treatment based on GC percentage is made."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="100" value="90" label="Maximal GC percentage threshold to conserve sequences" help=""/> + <param name='apply_max_GC_perc_content_filter_treatments' + type='boolean' checked="false" label="Filter + sequences with too high GC percentage?" + help="By default, no treatment based on + GC percentage is made."/> + <when value="true"> + <param name="max_GC_perc_content_filter_treatment_value" + type="integer" min="0" + max="100" value="90" label="Maximal GC + percentage threshold to conserve + sequences" help=""/> </when> </conditional> </when> </conditional> <conditional name="N_number_content_filter_treatments"> - <param name='apply_N_number_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their number of N bases?" help="By default, no treatment based on N number is made."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="10" label="Maximal N number threshold to conserve sequences" help=""/> + <param name='apply_N_number_content_filter_treatments' + type='boolean' checked="false" label="Filter + sequences based on their number of N bases?" + help="By default, no treatment based on N number + is made."/> + <when value="true"> + <param name="N_number_content_filter_treatment_value" + type="integer" min="0" + max="3000" value="10" label="Maximal N number + threshold to conserve sequences" help=""/> </when> </conditional> <conditional name="N_percentage_content_filter_treatments"> - <param name='apply_N_percentage_content_filter_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Filter sequences based on their percentage of N bases?" help="By default, sequences with more than 2% of N bases are removed."/> - <when value="yes"> - <param name="value" type="integer" min="0" max="100" value="2" label="Maximal N percentage threshold to conserve sequences" help=""/> + <param name='apply_N_percentage_content_filter_treatments' + type='boolean' checked="true" label="Filter sequences + based on their percentage of N bases?" help="By + default, sequences with more than 2% of N bases + are removed."/> + <when value="true"> + <param name="N_percentage_content_filter_treatment_value" + type="integer" min="0" max="100" + value="2" label="Maximal N percentage threshold + to conserve sequences" help=""/> </when> </conditional> - <param name='apply_other_base_content_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences with characters other than A, T, C, G and N?" help="By default, this treatment is not made."/> + <param name='apply_other_base_content_filter_treatments' + type='boolean' checked="false" label="Filter sequences + with characters other than A, T, C, G and N?" help="By + default, this treatment is not made."/> </when> </conditional> <conditional name="complexity_filter_treatments"> - <param name='apply_complexity_filter_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Filter sequences based on their complexity?" help="By default, no complexity filter is applied"/> - <when value="yes"> - <param name="method_complexity_filter_treatments" type="select" display="radio" label="Method to filter low complexity sequences" help=""> + <param name='apply_complexity_filter_treatments' type='boolean' + checked="false" label="Filter sequences based on their + complexity?" help="By default, no complexity filter is + applied"/> + <when value="true"> + <param name="method_complexity_filter_treatments" type="select" + display="radio" label="Method to filter low complexity + sequences" help=""> <option value="dust">Dust</option> <option value="entropy" >Entropy</option> </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."/> + <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."/> </when> </conditional> </when> </conditional> <conditional name="trimming_treatments"> - <param name='apply_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Apply trimming treatments?" help=""/> - <when value="yes"> + <param name='apply_trimming_treatments' type='boolean' checked="true" + label="Apply trimming treatments?" help=""/> + <when value="true"> <conditional name="length_trimming_treatments"> - <param name='apply_length_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim all sequences from the 3'-end to a length?" help="By default, no length trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Length of sequences after trimming" help=""/> + <param name='apply_length_trimming_treatments' type='boolean' + checked="false" label="Trim all sequences from the 3'-end + to a length?" help="By default, no length trimming is made"/> + <when value="true"> + <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" + value="100" label="Length of sequences after + trimming" help=""/> </when> </conditional> <conditional name="position_trimming_treatments"> - <param name='apply_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim all sequences from the ends?" help="By default, no position trimming is made"/> - <when value="yes"> + <param name='apply_position_trimming_treatments' type='boolean' + checked="false" label="Trim all sequences from the ends?" + help="By default, no position trimming is made"/> + <when value="true"> <conditional name="nb_position_trimming_treatments"> - <param name='apply_nb_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences by a defined number of positions?" help="By default, no position trimming is made"/> - <when value="yes"> + <param name='apply_nb_position_trimming_treatments' + type='boolean' checked="false" label="Trim sequences + by a defined number of positions?" help="By default, + no position trimming is made"/> + <when value="true"> <conditional name="left_position_trimming_treatments"> - <param name='apply_left_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 5'-end by a defined number of positions?" help="By default, no position trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 5'-end" help=""/> + <param name='apply_left_position_trimming_treatments' + type='boolean' checked="false" label="Trim + sequences at the 5'-end by a defined number + of positions?" help="By default, no position + trimming is made"/> + <when value="true"> + <param name="left_position_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Number of + positions to trim on 5'-end" help=""/> </when> </conditional> <conditional name="right_position_trimming_treatments"> - <param name='apply_right_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 3'-end by a defined number of positions?" help="By default, no position trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Number of positions to trim on 3'-end" help=""/> + <param name='apply_right_position_trimming_treatments' + type='boolean' checked="false" label="Trim + sequences at the 3'-end by a defined number + of positions?" help="By default, no position + trimming is made"/> + <when value="true"> + <param name="right_position_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Number + of positions to trim on 3'-end" + help=""/> </when> </conditional> </when> </conditional> <conditional name="percentage_position_trimming_treatments"> - <param name='apply_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/> - <when value="yes"> + <param name='apply_percentage_position_trimming_treatments' + type='boolean' checked="false" label="Trim sequences + by a defined percentage of read length?" help="By + default, no position trimming is made. The trim + length is rounded towards the lower integer"/> + <when value="true"> <conditional name="left_percentage_position_trimming_treatments"> - <param name='apply_left_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 5'-end by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 5'-end" help=""/> + <param name='apply_left_percentage_position_trimming_treatments' + type='boolean' checked="false" label="Trim + sequences at the 5'-end by a defined percentage + of read length?" help="By default, no position + trimming is made. The trim length is rounded + towards the lower integer"/> + <when value="true"> + <param name="left_percentage_position_trimming_treatment_value" + type="integer" min="0" + max="100" value="2" label="Percentage + of positions to trim on 5'-end" help=""/> </when> </conditional> <conditional name="right_percentage_position_trimming_treatments"> - <param name='apply_right_percentage_position_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequences at the 3'-end by a defined percentage of read length?" help="By default, no position trimming is made. The trim length is rounded towards the lower integer"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="100" value="2" label="Percentage of positions to trim on 3'-end" help=""/> + <param name='apply_right_percentage_position_trimming_treatments' + type='boolean' checked="false" label="Trim + sequences at the 3'-end by a defined percentage + of read length?" help="By default, no position + trimming is made. The trim length is rounded + towards the lower integer"/> + <when value="true"> + <param name="right_percentage_position_trimming_treatment_value" + type="integer" min="0" + max="100" value="2" label="Percentage + of positions to trim on 3'-end" help=""/> </when> </conditional> </when> @@ -327,38 +474,74 @@ </when> </conditional> <conditional name="tail_trimming_treatments"> - <param name='apply_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim tails?" help="By default, no tail trimming is made"/> - <when value="yes"> + <param name='apply_tail_trimming_treatments' type='boolean' + checked="false" label="Trim tails?" help="By default, no + tail trimming is made"/> + <when value="true"> <conditional name="a_t_tail_trimming_treatments"> - <param name='apply_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail?" help="By default, no poly-A/T tail trimming is made"/> - <when value="yes"> + <param name='apply_a_t_tail_trimming_treatments' + type='boolean' checked="false" label="Trim poly-A/T + tail?" help="By default, no poly-A/T tail trimming + is made"/> + <when value="true"> <conditional name="left_a_t_tail_trimming_treatments"> - <param name='apply_left_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail at the 5'-end?" help="By default, no 5'-end poly-A/T tail trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help=""/> + <param name='apply_left_a_t_tail_trimming_treatments' + type='boolean' checked="false" label="Trim + poly-A/T tail at the 5'-end?" help="By + default, no 5'-end poly-A/T tail trimming + is made"/> + <when value="true"> + <param name="left_a_t_tail_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Minimum + length of poly-A/T to trim at the 5'-end" + help=""/> </when> </conditional> <conditional name="right_a_t_tail_trimming_treatments"> - <param name='apply_right_a_t_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-A/T tail at the 5'-end?" help="By default, no 3'-end poly-A/T tail trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-A/T to trim at the 5'-end" help=""/> + <param name='apply_right_a_t_tail_trimming_treatments' + type='boolean' checked="false" label="Trim poly-A/T + tail at the 5'-end?" help="By default, no + 3'-end poly-A/T tail trimming is made"/> + <when value="true"> + <param name="right_a_t_tail_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Minimum + length of poly-A/T to trim at the 5'-end" + help=""/> </when> </conditional> </when> </conditional> <conditional name="ns_tail_trimming_treatments"> - <param name='apply_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail?" help="By default, no poly-N tail trimming is made"/> - <when value="yes"> + <param name='apply_ns_tail_trimming_treatments' type='boolean' + checked="false" label="Trim poly-N tail?" help="By + default, no poly-N tail trimming is made"/> + <when value="true"> <conditional name="left_ns_tail_trimming_treatments"> - <param name='apply_left_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail at the 5'-end?" help="By default, no 5'-end poly-N tail trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help=""/> + <param name='apply_left_ns_tail_trimming_treatments' + type='boolean' checked="false" label="Trim + poly-N tail at the 5'-end?" help="By default, + no 5'-end poly-N tail trimming is made"/> + <when value="true"> + <param name="left_ns_tail_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Minimum + length of poly-N to trim at the 5'-end" + help=""/> </when> </conditional> <conditional name="right_ns_tail_trimming_treatments"> - <param name='apply_right_ns_tail_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim poly-N tail at the 5'-end?" help="By default, no 3'-end poly-N tail trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="3000" value="100" label="Minimum length of poly-N to trim at the 5'-end" help=""/> + <param name='apply_right_ns_tail_trimming_treatments' + type='boolean' checked="false" label="Trim + poly-N tail at the 5'-end?" help="By default, + no 3'-end poly-N tail trimming is made"/> + <when value="true"> + <param name="right_ns_tail_trimming_treatment_value" + type="integer" min="0" + max="3000" value="100" label="Minimum + length of poly-N to trim at the 5'-end" + help=""/> </when> </conditional> </when> @@ -366,33 +549,62 @@ </when> </conditional> <conditional name="quality_trimming_treatments"> - <param name='apply_quality_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Trim sequence by quality score?" help="By default, a 3'-end trimming is made to remove ends with a minimum quality score over 5 bp below 20"/> - <when value="yes"> + <param name='apply_quality_trimming_treatments' type='boolean' + checked="true" label="Trim sequence by quality score?" + help="By default, a 3'-end trimming is made to remove ends + with a minimum quality score over 5 bp below 20"/> + <when value="true"> <conditional name="left_quality_trimming_treatments"> - <param name='apply_left_quality_trimming_treatments' type='boolean' checked="false" truevalue='yes' falsevalue='no' label="Trim sequence by quality score from the 5'-end?" help="By default, no 5'-end quality trimming is made"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help=""/> + <param name='apply_left_quality_trimming_treatments' + type='boolean' checked="false" label="Trim sequence + by quality score from the 5'-end?" help="By default, + no 5'-end quality trimming is made"/> + <when value="true"> + <param name="left_quality_trimming_treatment_value" + type="integer" min="0" max="40" + value="20" label="Quality score threshold to + trim positions" help=""/> </when> </conditional> <conditional name="right_quality_trimming_treatments"> - <param name='apply_right_quality_trimming_treatments' type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Trim sequence by quality score from the 3'-end?" help="By default, 3'-end trimming is made based on a score of 20"/> - <when value="yes"> - <param name="value" type="integer" min="0" max="40" value="20" label="Quality score threshold to trim positions" help=""/> + <param name='apply_right_quality_trimming_treatments' + type='boolean' checked="true" label="Trim sequence + by quality score from the 3'-end?" help="By default, + 3'-end trimming is made based on a score of 20"/> + <when value="true"> + <param name="right_quality_trimming_treatment_value" + type="integer" min="0" max="40" + value="20" label="Quality score threshold to + trim positions" help=""/> </when> </conditional> - <param name="type_quality_trimming_treatments" type="select" display="radio" label="Type of quality score calculation to use" help="By default, min is used"> + <param name="type_quality_trimming_treatments" type="select" + display="radio" label="Type of quality score calculation + to use" help="By default, min is used"> <option value="min" selected="true">Mininum</option> <option value="mean" >Mean</option> <option value="max" >Max</option> <option value="sum" >Sum</option> </param> - <param name="rule_quality_trimming_treatments" type="select" display="radio" label="Rule tu use to compare quality score to calculated value" help="By default, 'less than' is used"> + <param name="rule_quality_trimming_treatments" type="select" + display="radio" label="Rule tu use to compare quality + score to calculated value" help="By default, 'less than' + is used"> <option value="lt" selected="true">Less than</option> <option value="gt" >Greater than</option> <option value="et" >Equal to</option> </param> - <param name="window_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Size of the sliding window used to calculated quality score by type" help="To stop at the first base that fails the rule defined, use a window size of 1 (default value)"/> - <param name="step_quality_trimming_treatments" type="integer" min="0" max="300" value="1" label="Step size used to move the sliding window" help="To move the window over all quality scores without missing any, the step size sould be less or equal to the window size. The default value is 1."/> + <param name="window_quality_trimming_treatments" type="integer" + min="0" max="300" value="1" label="Size of the sliding + window used to calculated quality score by type" help="To + stop at the first base that fails the rule defined, use a + window size of 1 (default value)"/> + <param name="step_quality_trimming_treatments" type="integer" + min="0" max="300" value="1" label="Step size used to move + the sliding window" help="To move the window over all + quality scores without missing any, the step size sould + be less or equal to the window size. The default value + is 1."/> </when> </conditional> </when> @@ -400,13 +612,50 @@ </inputs> <outputs> - <data format="fastq" name="good_sequence_file" metadata_source="input_sequence_file"/> + <data format="fastq" name="good_sequence_file" + from_work_dir="good_sequences.fastq" + label="Good sequences of ${on_string} (PRINSEQ)" /> + <data format="fastq" name="rejected_sequence_file" + from_work_dir="rejected_sequences.fastq" + label="Rejected sequences of ${on_string} (PRINSEQ)" /> </outputs> <tests> <test> - <param name="input_sequence_file" value="input_sequences.fastq"/> - <output name="good_sequence_file" file="output_sequences.fastq"/> + <param name="sequence_to_control_file" 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="min_length_filter_treatment_value" value="60"/> + <param name='apply_max_length_filter_treatments' value="false" /> + <param name='apply_quality_filter_treatments' value="true"/> + <param name='apply_min_quality_filter_treatments' value="false" /> + <param name='apply_max_quality_filter_treatments' value="false"/> + <param name='apply_mean_quality_filter_treatments' value="true"/> + <param name='apply_min_mean_quality_filter_treatments' value="true"/> + <param name="min_mean_quality_filter_treatment_value" value="15"/> + <param name='apply_max_mean_quality_filter_treatments' value="false"/> + <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="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"/> + <param name='apply_trimming_treatments' value="true" /> + <param name='apply_length_trimming_treatments' value="false"/> + <param name='apply_position_trimming_treatments' value="false"/> + <param name='apply_tail_trimming_treatments' value="false"/> + <param name='apply_quality_trimming_treatments' value="true"/> + <param name='apply_left_quality_trimming_treatments' value="false"/> + <param name='apply_right_quality_trimming_treatments' value="true" /> + <param name="right_quality_trimming_treatment_value" value="20"/> + <param name="type_quality_trimming_treatments" value="min"/> + <param name="rule_quality_trimming_treatments" value="lt" /> + <param name="window_quality_trimming_treatments" value="1"/> + <param name="step_quality_trimming_treatments" value="1"/> + + <output name="good_sequence_file" file="good_sequences.fastq"/> </test> </tests> @@ -415,7 +664,7 @@ **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>`_. -----