--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_lncrna.xml	Tue Jul 17 11:49:16 2018 -0400
@@ -0,0 +1,181 @@
+<tool id="ctat_lncrna" name="ctat_lncrna" version="1.0.0" profile="17.05">
+
+    <description>Filters a high-quality set of lncRNA from reconstructed RNA-seq data</description>
+    <requirements>
+    <requirement type="package" version="1.0.1">ctat-lncrna</requirement>
+    </requirements>
+    <command detect_errors="default">
+      <![CDATA[
+     #if str($bedfile) != "":
+     lncrna --bedfile $bedfile
+     --config "${assembly.fields.path}" 
+     #end if
+
+     #if str($assembly) != "":
+         --assembly "${assembly.fields.value}"
+     #end if
+
+     #if $min_overlap != "":
+         --min_overlap "$min_overlap"
+     #end if
+
+     #if str($min_cluster) != "":
+         --min_cluster "$min_cluster"
+     #end if
+
+     #if str($min_coding) != "":
+         --min_coding "$min_coding"
+     #end if
+
+    #if str($minMatch) != "":
+        --minMatch "$minMatch"
+    #end if
+
+    #if str($pad) != "":
+        --pad "$pad"
+    #end if
+
+    #if str($gap_open) != "":
+        --gap_open "$gap_open"
+    #end if
+
+    #if str($gap_extend) != "":
+        --gap_extend "$gap_extend"
+    #end if
+    --web 
+    && cp -r slncky.EvolutionBrowser $html_file.files_path
+]]>
+    </command>
+
+    <inputs>
+      <param name="bedfile" format="interval" type="data" value="bedfile" label="Bed File:" help="Reconstructed transcripts (ex. from StringTie or Trinity)"/>
+      <param name="min_overlap" type="float" value="0.0" label="Min overlap" help="Remove any transcript that overlap annotated coding gene greater than min_overlap" />
+      <param name="min_cluster" type="integer" value="2" label="Min cluster" help="Minimum size of duplication clusters to remove" />
+      <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/>
+      <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" />
+      <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" />
+      <param name="gap_open" type="integer" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/>
+      <param name="gap_extend" type="integer" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/>
+      <param name="assembly" type="select" label="Choose annotation:" help="Select annotation">
+            <options from_data_table="ctat_lncrna_annotations" />
+      </param>
+    </inputs>
+
+    <outputs>
+           <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/>
+           <data format="tabular" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/>
+           <data format="tabular" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/>
+           <data format="tabular" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/>
+           <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/>
+           <data format="tabular" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/>
+           <data format="tabular" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/>
+           <data format="tabular" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/>
+           <data format="tabular" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/>
+    </outputs>
+
+    <stdio>
+          <exit_code range="1:" level="fatal" description="Error in SLNCky" />
+    </stdio>
+
+    <tests>
+        <test>
+            <param name="bedfile" value="reads.simPE.StringTie.transcripts.bed" />
+            <param name="assembly" value="hg19" /> 
+            <param name="min_overlap" value="0.0" />
+            <param name="min_cluster" value="2" />
+            <param name="min_coding" value="0.1" />
+            <param name="minMatch" value="0.1" />
+            <param name="pad" value="0" />
+            <param name="gap_open" value="200" />
+            <param name="gap_extend" value="40" />
+
+            <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
+            <output name="html_file" file="slncky/reads.simPE.browse.html" />
+
+            <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
+            <output name="canonical_to_lncs" file="slncky/reads.simPE.canonical_to_lncs.txt" />
+ 
+            <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
+            <output name="cluster_info" file="slncky/reads.simPE.cluster_info.txt" />
+
+            <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
+            <output name="filtered_info" file="slncky/reads.simPE.filtered_info.txt" />
+
+            <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
+            <output name="lncs" file="slncky/reads.simPE.lncs.bed" />
+
+            <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
+            <output name="lncs_info" file="slncky/reads.simPE.lncs.info.txt" />
+
+            <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
+            <output name="orfs" file="slncky/reads.simPE.orfs.txt" />
+
+            <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
+            <output name="orthologs_top" file="slncky/reads.simPE.orthologs.top.txt" />
+
+            <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
+            <output name="orthologs" file="slncky/reads.simPE.orthologs.txt" />
+
+        </test>
+        <test>
+            <param name="bedfile" value="mir-17-92.StringTie.transcripts.bed" />
+            <param name="assembly" value="hg19" /> 
+            <param name="min_overlap" value="0.0" />
+            <param name="min_cluster" value="2" />
+            <param name="min_coding" value="0.1" />
+            <param name="minMatch" value="0.1" />
+            <param name="pad" value="0" />
+            <param name="gap_open" value="200" />
+            <param name="gap_extend" value="40" />
+
+            <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
+            <output name="html_file" file="slncky/mir-17-92.browse.html" />
+
+            <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
+            <output name="canonical_to_lncs" file="slncky/mir-17-92.canonical_to_lncs.txt.sorted" sort="true" />
+ 
+            <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
+            <!-- This file isn't being created for some reason...
+            <output name="cluster_info" >
+                <assert_contents>
+                    <has_line_matching expression=".+" />
+                </assert_contents>
+            </output>
+            -->
+
+            <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
+            <output name="filtered_info" file="slncky/mir-17-92.filtered_info.txt.sorted" sort="true" />
+
+            <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
+            <output name="lncs" file="slncky/mir-17-92.lncs.bed" />
+
+            <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
+            <output name="lncs_info" file="slncky/mir-17-92.lncs.info.txt" />
+
+            <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
+            <output name="orfs" file="slncky/mir-17-92.orfs.txt" />
+
+            <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
+            <output name="orthologs_top" file="slncky/mir-17-92.orthologs.top.txt" />
+
+            <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
+            <output name="orthologs" file="slncky/mir-17-92.orthologs.txt" />
+        </test>
+    </tests>
+
+    <help>
+.. class:: infomark
+
+slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.
+
+To learn more about slncky visit their website_ .
+
+.. _website: https://github.com/slncky/slncky
+
+</help>
+
+<citations>
+        <citation type="doi">10.1186/s13059-016-0880-9</citation>
+</citations>
+
+</tool>