# HG changeset patch
# User refinery-platform
# Date 1441226270 14400
# Node ID 41e92972b7f1f660c0a1cb99f697e13b638df044

Fix XML formatting

diff -r 000000000000 -r 41e92972b7f1 emsar_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emsar_indices.loc.sample	Wed Sep 02 16:37:50 2015 -0400
@@ -0,0 +1,5 @@
+# EMSAR rsh files
+#
+# format of this .loc file (5 tab-separated columns):
+#value	dbkey	description	path to index?	path to rsh file
+#hg19	hg19	Human (hg19)	~/refs/hg19/EMSAR/RefSeq_hg19	~/refs/hg19/EMSAR/rsh/RefSeq.hg19.PE
diff -r 000000000000 -r 41e92972b7f1 emsar_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emsar_wrapper.xml	Wed Sep 02 16:37:50 2015 -0400
@@ -0,0 +1,91 @@
+<tool id="emsar" name="EMSAR" version="1.2j">
+    <description></description>
+
+    <command>
+
+    #set rsh_path = $refIndex.fields.rshPath
+    #set rsh = $rsh_path + "." + $nRL.__str__() + ".rsh"
+    #set libType = ""
+
+    #if $bPaired
+        #if $sLT.__str__() == "n"
+            #set libType = "ns"
+        #end if
+        #if $sLT.__str__() == "f"
+            #set libType = "ssfr"
+        #end if
+        #if $sLT.__str__() == "r"
+            #set libType = "ssrf"
+        #end if
+    #else
+        #if $sLT.__str__() == "n"
+            #set libType = "ns"
+        #end if
+        #if $sLT.__str__() == "f"
+            #set libType = "ssf"
+        #end if
+        #if $sLT.__str__() == "r"
+            #set libType = "ssr"
+        #end if
+    #end if
+
+    emsar
+        -P
+        #if $sBS.__str__() == "S"
+        -S
+        #end if
+        #if $sBS.__str__() == "B"
+        -B
+        #end if
+        -p 8
+        -h $sHT
+        #if $bG
+        -g
+        #end if
+        -s $libType
+        -I $rsh
+        output
+        emsar
+        $input_bam
+        2> emsar.log
+
+    </command>
+
+    <stdio></stdio>
+
+    <inputs>
+        <param format="bam,sam" compression="none" name="input_bam" type="data" label="Bowtie Alignment BAM file" help=""/>
+        <param name="refIndex" type="select" label="Select a reference genome" help="">
+            <options from_data_table="emsar_indices">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No genomes are available for the selected input dataset"/>
+            </options>
+        </param>
+        <param name="sBS" type="select" label="Input alignment file type ">
+            <option value="S">SAM</option>
+            <option value="B">BAM</option>
+        </param>
+        <param name="sHT" type="select" label="Transcriptome header type">
+            <option value="R">RefSeq</option>
+            <option value="E">Ensembl</option>
+        </param>
+        <param name="bG" type="boolean" label="Generate list of all segments with their associated sequence-sharing set and transcript(seperated by '+')" value="True" />
+        <param name="bPaired" type="boolean" label="Is this paired-end sequenced data ?" value="True" />
+        <param name="nRL" type="integer" label="read length" value="101" />
+        <param name="sLT" type="select" label="library type">
+            <option value="n">Unstranded</option>
+            <option value="f">Forward Stranded</option>
+            <option value="r">Reverse Stranded</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="fpkm" label="${tool.name} on ${on_string}: FPKM" from_work_dir="output/emsar.0.fpkm" />
+        <data format="txt" name="fraglength_stat" label="${tool.name} on ${on_string}: Fracgment Length Effect" from_work_dir="output/emsar.0.fraglength_effect" />
+        <data format="txt" name="segments" label="${tool.name} on ${on_string}: Segments" from_work_dir="output/emsar.0.segments" />
+    </outputs>
+
+    <help>
+
+    </help>
+</tool>
diff -r 000000000000 -r 41e92972b7f1 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Sep 02 16:37:50 2015 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="emsar_indices" comment_char="#">
+        <columns>value, dbkey, name, idxPath, rshPath</columns>
+        <file path="emsar_indices.loc" />
+    </table>
+</tables>