diff rmarkdown_report.xml @ 1:e0828838e0f3 draft default tip

update

--- a/rmarkdown_report.xml	Fri Nov 09 13:29:21 2018 -0500
+++ b/rmarkdown_report.xml	Fri Nov 09 15:25:01 2018 -0500
@@ -23,20 +23,21 @@
             -d $report.files_path
 
             -A $input_fasta
-            -B $level
-            -C $linker
-            -D $input_format
-            -E $output_format
-            -F $parse_seqids
+            -B $window_length
+            -C $level
+            -D $linker
+            -E $input_format
+            -F $output_format
+            -G $parse_seqids
 
-            -G $out
+            -H $out
 
 
 ]]></command>
   <inputs>
-    <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs>
+    <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="fasta" selected="true">fasta</option><option value="blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="acclist" selected="false">acclist</option><option value="fasta" selected="true">fasta</option><option value="interval" selected="false">interval</option><option value="maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="maskinfo_xml" selected="false">maskinfo_xml</option><option value="seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs>
   <outputs>
-        <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs>
+        <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" format="fasta" label="${tool.name} on ${on_string}" hidden="false"/></outputs>
   <citations>
         <citation type="bibtex"><![CDATA[
             @article{allaire2016rmarkdown,