Repository 'tetoolkit_tetranscripts'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts

Changeset 2:bbeab8445490 (2020-10-04)
Previous changeset 1:bf4ee2810759 (2020-07-16) Next changeset 3:313414e9abcf (2020-10-08)
Commit message:
"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
modified:
tetranscript.xml
b
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
[
b'@@ -1,57 +1,58 @@\n <?xml version="1.0"?>\n-<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy0">\n+<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n     <description>annotates reads to genes and transposable elements</description>\n     <macros>\n-        <token name="@TOOL_VERSION@">2.2.0</token>\n+        <token name="@TOOL_VERSION@">2.2.1</token>\n+        <token name="@VERSION_SUFFIX@">0</token>\n     </macros>\n     <requirements>\n         <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement>\n     </requirements>\n     <version_command>TEtranscripts --version</version_command>\n     <command detect_errors="exit_code"><![CDATA[\n-        ## initialize\n-        ## file extension is required\n-        ln -s \'$GTF\' \'gene_annotation.gtf\' &&\n-        ln -s \'$TE\' \'transposable_annotation.gtf\' &&\n+## initialize\n+## file extension is required\n+ln -s \'$GTF\' \'gene_annotation.gtf\' &&\n+ln -s \'$TE\' \'transposable_annotation.gtf\' &&\n \n-        ## run\n-        TEtranscripts\n-            ## required\n-            -t\n-            #for $s in $sample_rep\n-                \'${s.t}\'\n-            #end for\n-            -c\n-            #for $s in $sample_rep\n-                \'${s.c}\'\n-            #end for\n-            --GTF \'gene_annotation.gtf\'\n-            --TE \'transposable_annotation.gtf\'\n-            ## optional\n-            --stranded \'$io.stranded\'\n-            $io.sortByPos\n-            --project \'result\'\n-            --mode \'$ap.mode\'\n-            --minread $ap.minread\n-            #if $ap.fragmentLength\n-                --fragmentLength $ap.fragmentLength\n-            #end if\n-            --iteration $ap.iteration\n-            --padj $ap.padj\n-            --foldchange $ap.foldchange\n-            #if \'log\' in $ap.out\n-                --verbose 3\n-                |& tee log.txt\n-            #end if\n+## run\n+TEtranscripts\n+## required\n+-t\n+#for $s in $sample_rep\n+    \'${s.t}\'\n+#end for\n+-c\n+#for $s in $sample_rep\n+    \'${s.c}\'\n+#end for\n+--GTF \'gene_annotation.gtf\'\n+--TE \'transposable_annotation.gtf\'\n+## optional\n+--stranded \'$io.stranded\'\n+$io.sortByPos\n+--project \'result\'\n+--mode \'$ap.mode\'\n+--minread $ap.minread\n+#if $ap.fragmentLength\n+    --fragmentLength $ap.fragmentLength\n+#end if\n+--iteration $ap.iteration\n+--padj $ap.padj\n+--foldchange $ap.foldchange\n+#if \'log\' in $oo.out\n+    --verbose 3\n+    |& tee \'$out_log\'\n+#end if\n         ]]></command>\n     <inputs>\n         <repeat name="sample_rep" min="2" title="Select input data">\n             <param argument="-t" type="data" format="bam" label="Treatment sample file"/>\n             <param argument="-c" type="data" format="bam" label="Control sample file"/>\n         </repeat>\n-        <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/>\n-        <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/>\n-        <section name="io" title="Input options">\n+        <param argument="--GTF" type="data" format="gtf" label="Select file for gene annotations"/>\n+        <param argument="--TE" type="data" format ="gtf" label="Select file for transposable element annotations"/>\n+        <section name="io" title="Input options" expanded="true">\n             <param argument="--stranded" type="select" label="Select library type">\n                 <option value="no">Library is unstranded (no)</option>\n                 <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option>\n@@ -69,30 +70,32 @@\n             <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/>\n             <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/>\n             <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-cha'..b'            <param name="out" value="cnttable,deseq2,gta,sgt,log"/>\n             </section>\n             <output name="out_cnt">\n                 <assert_contents>\n                     <has_n_lines n="295"/>\n-                    <!-- depends on sample names -->\n                     <has_text_matching expression="gene.+"/>\n-                    <!-- order changes -->\n                     <has_text_matching expression="TIRANT.+"/>\n                 </assert_contents>\n             </output>\n@@ -194,20 +178,18 @@\n                     <has_text_matching expression="data.+"/>\n                 </assert_contents>\n             </output>\n+            <output name="out_gta">\n+                <assert_contents>\n+                    <has_n_lines n="3"/>\n+                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>\n+                    <has_text_matching expression="DNAREP1.+"/>\n+                </assert_contents>\n+            </output>\n             <output name="out_log">\n                 <assert_contents>\n                     <has_text_matching expression="INFO.+"/>\n                 </assert_contents>\n             </output>\n-            <output name="out_gta">\n-                <assert_contents>\n-                    <has_n_lines n="3"/>\n-                    <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>\n-                    <!-- order changes -->\n-                    <has_text_matching expression="DNAREP1.+"/>\n-                </assert_contents>\n-            </output>\n-            <!-- no content, test dataset to small -->\n             <output name="out_sgt">\n                 <assert_contents>\n                     <has_n_lines n="1"/>\n@@ -230,15 +212,13 @@\n             <section name="io">\n                 <param name="stranded" value="reverse"/>\n             </section>\n-            <section name="ap">\n+            <section name="oo">\n                 <param name="out" value="cnttable,deseq2,gta,sgt,log"/>\n             </section>\n             <output name="out_cnt">\n                 <assert_contents>\n                     <has_n_lines n="295"/>\n-                    <!-- depends on sample names -->\n                     <has_text_matching expression="gene.+"/>\n-                    <!-- order changes -->\n                     <has_text_matching expression="TIRANT.+"/>\n                 </assert_contents>\n             </output>\n@@ -248,19 +228,18 @@\n                     <has_text_matching expression="data.+"/>\n                 </assert_contents>\n             </output>\n-            <output name="out_log">\n-                <assert_contents>\n-                    <has_text_matching expression="INFO.+"/>\n-                </assert_contents>\n-            </output>\n             <output name="out_gta">\n                 <assert_contents>\n                     <has_n_lines n="23"/>\n                     <has_line line="baseMean&#009;log2FoldChange&#009;lfcSE&#009;stat&#009;pvalue&#009;padj"/>\n-                    <!-- order changes -->\n                     <has_text_matching expression="TART.+"/>\n                 </assert_contents>\n             </output>\n+            <output name="out_log">\n+                <assert_contents>\n+                    <has_text_matching expression="INFO.+"/>\n+                </assert_contents>\n+            </output>\n             <output name="out_sgt">\n                 <assert_contents>\n                     <has_n_lines n="2"/>\n@@ -289,7 +268,7 @@\n \n **References**\n \n-More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_.\n+More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `GitHub <https://github.com/mhammell-laboratory/TEtranscripts>`_.\n     ]]></help>\n     <citations>\n         <citation type="doi">10.1093/bioinformatics/btv422</citation>\n'