# HG changeset patch
# User iuc
# Date 1601805229 0
# Node ID bbeab8445490e44329dad35165af2a4a2acaab06
# Parent  bf4ee2810759bc184fecf23ac10e48da3d2bd51d
"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"

diff -r bf4ee2810759 -r bbeab8445490 tetranscript.xml
--- a/tetranscript.xml	Thu Jul 16 08:04:29 2020 -0400
+++ b/tetranscript.xml	Sun Oct 04 09:53:49 2020 +0000
@@ -1,57 +1,58 @@
 <?xml version="1.0"?>
-<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy0">
+<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>annotates reads to genes and transposable elements</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.2.0</token>
+        <token name="@TOOL_VERSION@">2.2.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement>
     </requirements>
     <version_command>TEtranscripts --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        ## initialize
-        ## file extension is required
-        ln -s '$GTF' 'gene_annotation.gtf' &&
-        ln -s '$TE' 'transposable_annotation.gtf' &&
+## initialize
+## file extension is required
+ln -s '$GTF' 'gene_annotation.gtf' &&
+ln -s '$TE' 'transposable_annotation.gtf' &&
 
-        ## run
-        TEtranscripts
-            ## required
-            -t
-            #for $s in $sample_rep
-                '${s.t}'
-            #end for
-            -c
-            #for $s in $sample_rep
-                '${s.c}'
-            #end for
-            --GTF 'gene_annotation.gtf'
-            --TE 'transposable_annotation.gtf'
-            ## optional
-            --stranded '$io.stranded'
-            $io.sortByPos
-            --project 'result'
-            --mode '$ap.mode'
-            --minread $ap.minread
-            #if $ap.fragmentLength
-                --fragmentLength $ap.fragmentLength
-            #end if
-            --iteration $ap.iteration
-            --padj $ap.padj
-            --foldchange $ap.foldchange
-            #if 'log' in $ap.out
-                --verbose 3
-                |& tee log.txt
-            #end if
+## run
+TEtranscripts
+## required
+-t
+#for $s in $sample_rep
+    '${s.t}'
+#end for
+-c
+#for $s in $sample_rep
+    '${s.c}'
+#end for
+--GTF 'gene_annotation.gtf'
+--TE 'transposable_annotation.gtf'
+## optional
+--stranded '$io.stranded'
+$io.sortByPos
+--project 'result'
+--mode '$ap.mode'
+--minread $ap.minread
+#if $ap.fragmentLength
+    --fragmentLength $ap.fragmentLength
+#end if
+--iteration $ap.iteration
+--padj $ap.padj
+--foldchange $ap.foldchange
+#if 'log' in $oo.out
+    --verbose 3
+    |& tee '$out_log'
+#end if
         ]]></command>
     <inputs>
         <repeat name="sample_rep" min="2" title="Select input data">
             <param argument="-t" type="data" format="bam" label="Treatment sample file"/>
             <param argument="-c" type="data" format="bam" label="Control sample file"/>
         </repeat>
-        <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/>
-        <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/>
-        <section name="io" title="Input options">
+        <param argument="--GTF" type="data" format="gtf" label="Select file for gene annotations"/>
+        <param argument="--TE" type="data" format ="gtf" label="Select file for transposable element annotations"/>
+        <section name="io" title="Input options" expanded="true">
             <param argument="--stranded" type="select" label="Select library type">
                 <option value="no">Library is unstranded (no)</option>
                 <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option>
@@ -69,30 +70,32 @@
             <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/>
             <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/>
             <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-change ratio (absolute) cutoff for differential expression"/>
-            <param name="out" type="select" multiple="true" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied.">
+        </section>
+        <section name="oo" title="Output options">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied.">
                 <option value="cnttable" selected="true">cntTable</option>
-                <option value="deseq2" selected="true">DESeq2.R</option>
+                <option value="deseq2">DESeq2.R</option>
                 <option value="gta" selected="true">Gene TE Analysis</option>
+                <option value="log">Log</option>
                 <option value="sgt" selected="true">SigDiff Gene TE</option>
-                <option value="log">Log</option>
             </param>
         </section>
     </inputs>
     <outputs>
         <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable">
-            <filter>'cnttable' in ap['out']</filter>
+            <filter>'cnttable' in oo['out']</filter>
         </data>
         <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R">
-            <filter>'deseq2' in ap['out']</filter>
+            <filter>'deseq2' in oo['out']</filter>
+        </data>
+        <data name="out_gta" format="tabular" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis">
+            <filter>'gta' in oo['out']</filter>
         </data>
         <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log">
-            <filter>'log' in ap['out']</filter>
+            <filter>'log' in oo['out']</filter>
         </data>
-        <data name="out_gta" format="txt" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis">
-            <filter>'gta' in ap['out']</filter>
-        </data>
-        <data name="out_sgt" format="txt" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE">
-            <filter>'sgt' in ap['out']</filter>
+        <data name="out_sgt" format="tabular" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE">
+            <filter>'sgt' in oo['out']</filter>
         </data>
     </outputs>
     <tests>
@@ -103,7 +106,7 @@
         -->
 
         <!-- #1: default -->
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="3">
             <repeat name="sample_rep">
                 <param name="t" value="treatment1.bam"/>
                 <param name="c" value="control1.bam"/>
@@ -114,39 +117,20 @@
             </repeat>
             <param name="GTF" value="gtf.gtf"/>
             <param name="TE" value="te.gtf"/>
-            <section name="ap">
-                <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
-            </section>
             <output name="out_cnt">
                 <assert_contents>
                     <has_n_lines n="295"/>
-                    <!-- depends on sample names -->
                     <has_text_matching expression="gene.+"/>
-                    <!-- order changes -->
                     <has_text_matching expression="TIRANT.+"/>
                 </assert_contents>
             </output>
-            <output name="out_deseq2">
-                <assert_contents>
-                    <has_n_lines n="14"/>
-                    <has_text_matching expression="data.+"/>
-                </assert_contents>
-            </output>
-            <output name="out_log">
-                <assert_contents>
-                    <has_text_matching expression="INFO"/>
-                    <has_text_matching expression=".+Done"/>
-                </assert_contents>
-            </output>
             <output name="out_gta">
                 <assert_contents>
                     <has_n_lines n="71"/>
                     <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
-                    <!-- order changes -->
                     <has_text_matching expression="TIRANT.+"/>
                 </assert_contents>
             </output>
-            <!-- no content, test dataset to small -->
             <output name="out_sgt">
                 <assert_contents>
                     <has_n_lines n="1"/>
@@ -177,14 +161,14 @@
                 <param name="iteration" value="90"/>
                 <param name="padj" value="0.06"/>
                 <param name="foldchange" value="2.0"/>
+            </section>
+            <section name="oo">
                 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
             </section>
             <output name="out_cnt">
                 <assert_contents>
                     <has_n_lines n="295"/>
-                    <!-- depends on sample names -->
                     <has_text_matching expression="gene.+"/>
-                    <!-- order changes -->
                     <has_text_matching expression="TIRANT.+"/>
                 </assert_contents>
             </output>
@@ -194,20 +178,18 @@
                     <has_text_matching expression="data.+"/>
                 </assert_contents>
             </output>
+            <output name="out_gta">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
+                    <has_text_matching expression="DNAREP1.+"/>
+                </assert_contents>
+            </output>
             <output name="out_log">
                 <assert_contents>
                     <has_text_matching expression="INFO.+"/>
                 </assert_contents>
             </output>
-            <output name="out_gta">
-                <assert_contents>
-                    <has_n_lines n="3"/>
-                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
-                    <!-- order changes -->
-                    <has_text_matching expression="DNAREP1.+"/>
-                </assert_contents>
-            </output>
-            <!-- no content, test dataset to small -->
             <output name="out_sgt">
                 <assert_contents>
                     <has_n_lines n="1"/>
@@ -230,15 +212,13 @@
             <section name="io">
                 <param name="stranded" value="reverse"/>
             </section>
-            <section name="ap">
+            <section name="oo">
                 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>
             </section>
             <output name="out_cnt">
                 <assert_contents>
                     <has_n_lines n="295"/>
-                    <!-- depends on sample names -->
                     <has_text_matching expression="gene.+"/>
-                    <!-- order changes -->
                     <has_text_matching expression="TIRANT.+"/>
                 </assert_contents>
             </output>
@@ -248,19 +228,18 @@
                     <has_text_matching expression="data.+"/>
                 </assert_contents>
             </output>
-            <output name="out_log">
-                <assert_contents>
-                    <has_text_matching expression="INFO.+"/>
-                </assert_contents>
-            </output>
             <output name="out_gta">
                 <assert_contents>
                     <has_n_lines n="23"/>
                     <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>
-                    <!-- order changes -->
                     <has_text_matching expression="TART.+"/>
                 </assert_contents>
             </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression="INFO.+"/>
+                </assert_contents>
+            </output>
             <output name="out_sgt">
                 <assert_contents>
                     <has_n_lines n="2"/>
@@ -289,7 +268,7 @@
 
 **References**
 
-More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_.
+More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `GitHub <https://github.com/mhammell-laboratory/TEtranscripts>`_.
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv422</citation>