rgrnastar: rg_rnaStar.xml comparison

comparison rg_rnaStar.xml @ 7:a70a7eebb435 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c

author	iuc
date	Wed, 16 May 2018 17:31:03 -0400
parents	2055c2667eb3
children	d5659efd66aa

comparison

equal deleted inserted replaced

-:2055c2667eb3
+:a70a7eebb435
-<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
+<tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01">
 <description>Gapped-read mapper for RNA-seq data</description>
 <macros>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 #end if
 ## Output parameters
 #if str( $output_params.output_select ) == "yes":
 --outSAMattributes $output_params.outSAMattributes
---outSAMstrandField $output_params.outSAMstrandField
+#if str( $params.settingsType ) != "star_fusion":
+--outSAMstrandField $output_params.outSAMstrandField
+#end if
 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
+--outFilterIntronStrands $output_params.outFilterIntronStrands
 #if str( $output_params.output_params2.output_select2 ) == "yes":
 --outSAMunmapped $output_params.output_params2.outSAMunmapped
 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique"
 --outFilterType $output_params.output_params2.outFilterType
 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax"
 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin"
 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
+--outSAMmultNmax "$output_params.output_params2.outSAMmultNmax"
+--outSAMtlen "$output_params.output_params2.outSAMtlen"
+--outBAMsortingBinsN "$output_params.output_params2.outBAMsortingBinsN"
 #end if
 #end if
 ## Other parameters
 #if str( $params.settingsType ) == "star_fusion":
 --alignSJDBoverhangMin 10
 --alignMatesGapMax 200000
 --alignIntronMax 200000
 --twopassMode Basic
 --twopass1readsN -1
+--chimSegmentReadGapMax 3
-## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
+--alignSJstitchMismatchNmax 5 -1 5 5
-## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0
+--outSAMstrandField intronMotif
 #elif str( $params.settingsType ) == "full":
 ## Extended parameter options
 ## Seed parameter options
 --twopass1readsN "$params.twopass.twopass1readsN"
 #end if
 ## Chimeric alignment parameter options
 #if str( $params.chim.chim_select ) == "yes":
+--chimOutType Junctions SeparateSAMold
 --chimSegmentMin "$params.chim.chimSegmentMin"
 --chimScoreMin "$params.chim.chimScoreMin"
 --chimScoreDropMax "$params.chim.chimScoreDropMax"
 --chimScoreSeparation "$params.chim.chimScoreSeparation"
 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
+--chimMainSegmentMultNmax "$params.chim.chimMainSegmentMultNmax"
+--chimMultimapNmax "$params.chim.chimMultimapNmax"
+--chimMultimapScoreRange "$params.chim.chimMultimapScoreRange"
 #end if
 ## Limits
 --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
 --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"
 #end if
 ## Convert chimeric reads.
-#if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
+#if str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0:
 &&
-samtools view
+samtools sort -@ \${GALAXY_SLOTS:-4} -o ChimericSorted.bam -O BAM Chimeric.out.sam
--@ \${GALAXY_SLOTS:-4}
--Shb Chimeric.out.sam |
-samtools sort
--@ \${GALAXY_SLOTS:-4} - ChimericSorted
 #end if
 ]]></command>
 <inputs>
 <!-- FASTQ input(s) and options specifically for paired-end data. -->
 </param>
 <param argument="--outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended">
 <option value="None" selected="true">No</option>
 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
+</param>
+<param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands">
+<option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option>
+<option value="None">No filtering</option>
 </param>
 <!-- Additional output parameter settings. -->
 <conditional name="output_params2">
 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
+<param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" />
+<param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
+<option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
+<option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
+</param>
+<param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50."/>
 </when>
 <when value="no"/>
 </conditional>
 </when>
 <when value="no"/>
 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/>
 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
+<param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10" label="Maximum number of multi-alignments for the main chimeric segment." help="A value of 1 prohibits multimapping main segments"/>
+<param argument="--chimMultimapNmax" type="integer" min="0" value="0" label="Maximum number of chimeric multi-alignments" help="A value of 0 (the default) only considers unique alignments" />
+<param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" label="Score range for multi-mapping chimeras" help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
 </when>
 <when value="no"/>
 </conditional>
 </when>
 </conditional>
 </conditional>
 </actions>
 </data>
 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
-<filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
+<filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter>
 <actions>
 <conditional name="refGenomeSource.geneSource">
 <when value="indexed">
 <action type="metadata" name="dbkey">
 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
 jI: Start and end of introns for all junctions
 **STAR-Fusion**
 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
-STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
+STAR prior to STAR-Fusion can be pre-selected.
---chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
---alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0
 **Attributions**
 rna_star - see the web site at rna_star_

Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 7:a70a7eebb435 draft