# HG changeset patch
# User mingchen0919
# Date 1514472446 18000
# Node ID 116bd227a9d8d8e870a14f5c9851bb7ce615d28e
# Parent  51dfced124049855121044d2e7d432846ee259bc
create tool

diff -r 51dfced12404 -r 116bd227a9d8 rmarkdown_feature_counts.xml
--- a/rmarkdown_feature_counts.xml	Thu Dec 28 09:44:46 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 09:47:26 2017 -0500
@@ -36,7 +36,7 @@
     <param type="text" name="read_2_pos" label="read2pos" help="Specifying whether each read should be reduced to its 5' most base or 3' most base. It has three possible values: NULL, 5 (denoting 5' most base) and 3 (denoting 3' most base). The default value is NULL. With the default value, the whole read is used for summarization. When read2pos is set to 5 (or 3), read summarization will be performed based on the 5' (or 3') most base position. read2pos can be used together with readExtension5 and readExtension3 parameters to set any desired length for reads." optional="False" value="NULL"/>
     <param type="boolean" name="count_multi_mapping_reads" label="countMultiMappingReads" help="logical indicating if multi-mapping reads/fragments should be counted, FALSE by default. If TRUE, a multi-mapping read will be counted up to N times if it has N reported mapping locations. This function uses the 'NH' tag to find multi-mapping reads." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
     <param type="boolean" name="fraction" label="fraction" help="logical indicating if fractional counts will be produced for multi-mapping reads. If TRUE, a fractional count, 1/n, will be generated for each reported alignment of a multi-mapping read, where n is the total number of alignments reported for that read. countMultiMappingReads must be set to TRUE when fraction is TRUE." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="integer" name="min_mqs" label="minMQS" help="integer giving the minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." optional="False"/>
+    <param type="integer" name="min_mqs" label="minMQS" help="integer giving the minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." optional="False" value="0"/>
     <param type="boolean" name="split_only" label="splitOnly" help="logical indicating whether only split alignments (their CIGAR strings contain letter 'N') should be included for summarization. FALSE by default. Example split alignments are exon-spanning reads from RNA-seq data. useMetaFeatures should be set to FALSE and allowMultiOverlap should be set to TRUE, if the purpose of summarization is to assign exon-spanning reads to all their overlapping exons." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
     <param type="boolean" name="non_split_only" label="nonSplitOnly" help="logical indicating whether only non-split alignments (their CIGAR strings do not contain letter 'N') should be included for summarization. FALSE by default." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
     <param type="boolean" name="primary_only" label="primaryOnly" help="logical indicating if only primary alignments should be counted. Primary and secondary alignments are identified using bit 0x100 in the Flag field of SAM/BAM files. If TRUE, all primary alignments in a dataset will be counted no matter they are from multi-mapping reads or not (ie. countMultiMappingReads is ignored)." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>