changeset 2:51dfced12404 draft

create tool

--- a/rmarkdown_feature_counts.xml	Thu Dec 28 09:38:30 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 09:44:46 2017 -0500
@@ -31,8 +31,8 @@
     <param type="boolean" name="allow_multi_overlap" label="allowMultiOverlap" help="logical indicating if a read is allowed to be assigned to more than one feature (or meta-feature) if it is found to overlap with more than one feature (or meta-feature). FALSE by default." optional="False" truevalue="TRUE" falsevalue="FALSE"/>
     <param type="integer" name="min_overlap" label="minOverlap" help="integer giving the minimum number of overlapped bases required for assigning a read to a feature (or a meta-feature). For assignment of read pairs (fragments), numbers of overlapping bases from each read in the same pair will be summed. If a negative value is provided, the read will be extended from both ends. 1 by default." optional="False" value="1"/>
     <param type="boolean" name="largest_overlap" label="largestOverlap" help="If TRUE, a read (or read pair) will be assigned to the feature (or meta-feature) that has the largest number of overlapping bases, if the read (or read pair) overlaps with multiple features (or meta-features)." optional="False" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="integer" name="read_extension_5" label="readExtension5" help="integer giving the number of bases extended upstream from 5' end of each read. 0 by default." optional="False"/>
-    <param type="integer" name="read_extension_3" label="readExtension3" help="integer giving the number of bases extended downstream from 3' end of each read. 0 by default." optional="False"/>
+    <param type="integer" name="read_extension_5" label="readExtension5" help="integer giving the number of bases extended upstream from 5' end of each read. 0 by default." optional="False" value="0"/>
+    <param type="integer" name="read_extension_3" label="readExtension3" help="integer giving the number of bases extended downstream from 3' end of each read. 0 by default." optional="False" value="0"/>
     <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"/>
@@ -70,15 +70,15 @@
                         volume={6},
                         year={2016}
                     ]]></citation>
-    <citation type="bibtex"><![CDATA[@article{liao2013featurecounts,
-  title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
-  author={Liao, Yang and Smyth, Gordon K and Shi, Wei},
-  journal={Bioinformatics},
-  volume={30},
-  number={7},
-  pages={923--930},
-  year={2013},
-  publisher={Oxford University Press}
+    <citation type="bibtex"><![CDATA[@article{liao2013featurecounts,
+  title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
+  author={Liao, Yang and Smyth, Gordon K and Shi, Wei},
+  journal={Bioinformatics},
+  volume={30},
+  number={7},
+  pages={923--930},
+  year={2013},
+  publisher={Oxford University Press}
 }]]></citation>
   </citations>
 </tool>