# HG changeset patch
# User rnateam
# Date 1480447980 18000
# Node ID a56343c142d5ef940f89d9a0d5dea53254d317e3
# Parent  93b90466d5336ef0832b0cd0abe6d113ad88b78b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf

diff -r 93b90466d533 -r a56343c142d5 readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Nov 29 14:33:00 2016 -0500
@@ -0,0 +1,10 @@
+Important notes
+----------------
+
+- At least 2 cores should be used for running ``ribotaper part 3: ribosome profiling``,  therefore please configure **job_conf.xml** accordingly.
+
+- We ran the RiboTaper analysis on an SGE cluster, using 7 cores and h_vmem 8G. For each dataset, the complete RiboTaper workflow (from the bam files to final results) took ~ 1 day.
+
+- The current RiboTaper framework is not designed to identify and quantify ORFs on different transcripts. This means the transcript annotation is crucial.
+
+- Be careful about using scaffolds, both in the genome and GTF files, which may slow the whole pipeline.
diff -r 93b90466d533 -r a56343c142d5 ribotaper_part1_create_annotation_files.xml
--- a/ribotaper_part1_create_annotation_files.xml	Tue Jun 07 17:49:46 2016 -0400
+++ b/ribotaper_part1_create_annotation_files.xml	Tue Nov 29 14:33:00 2016 -0500
@@ -1,6 +1,6 @@
 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="0.1.0">
     <requirements>
-            <requirement type="package" version="1.3.1">ribotaper</requirement>
+            <requirement type="package" version="1.3.1a">ribotaper</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -13,9 +13,7 @@
             "$ccdsid"
             "$appris"
             "annotation_path"
-
         &&
-
         tar
             "czvf"
             "$output2"
@@ -37,7 +35,7 @@
     </inputs>
     <outputs>
         <data name="output1" type="data" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="start_stops_FAR"/>
-        <data name="output2" type="data" format="compressed_archive" label="annotation_path"/>
+        <data name="output2" type="data" format="zip" label="annotation_path"/>
     </outputs>
     <tests>
         <test>
@@ -81,12 +79,14 @@
 ``Ribotaper part 1`` generates two files:
 
   - **start_stops_FAR** in BED format
-  - **annotation_path**  in format of compressed archive
+  - **annotation_path**  in format of zip
 
 *Start_stops_FAR*
 is used as an input for ``ribotaper part 2``.
 *Annotation_path*
 is used as an input for ``ribotaper part 3``.
+
+
 ]]></help>
     <citations>
         <citation type="doi">10.1038/nmeth.3688</citation>
diff -r 93b90466d533 -r a56343c142d5 ribotaper_part2_create_metaplots.xml
--- a/ribotaper_part2_create_metaplots.xml	Tue Jun 07 17:49:46 2016 -0400
+++ b/ribotaper_part2_create_metaplots.xml	Tue Nov 29 14:33:00 2016 -0500
@@ -1,6 +1,6 @@
 <tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0">
     <requirements>
-            <requirement type="package" version="1.3.1">ribotaper</requirement>
+            <requirement type="package" version="1.3.1a">ribotaper</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
diff -r 93b90466d533 -r a56343c142d5 ribotaper_part3_main.xml
--- a/ribotaper_part3_main.xml	Tue Jun 07 17:49:46 2016 -0400
+++ b/ribotaper_part3_main.xml	Tue Nov 29 14:33:00 2016 -0500
@@ -1,6 +1,6 @@
 <tool id="ribotaper_ribosome_profiling" name="ribotaper part 3: ribosome profiling" version="0.1.0">
     <requirements>
-            <requirement type="package" version="1.3.1">ribotaper</requirement>
+            <requirement type="package" version="1.3.1a">ribotaper</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -17,24 +17,19 @@
             "$ribo_bam"
             "$rna_bam"
             "annotation_path"
-            "$read_lenghts_ribo1,$read_lenghts_ribo2,$read_lenghts_ribo3"
-            "$cutoff1,$cutoff2,$cutoff3"
+            "$read_lenghts_ribo"
+            "$cutoff"
             "\${GALAXY_SLOTS:-12}"
 
     ]]></command>
     <inputs>
-        <param name="annotation_path" type="data" format="compressed_archive" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
+        <param name="annotation_path" type="data" format="zip" label="annotation_path" help="Please run 'ribotaper part 1' to generate the archive."/>
         <param name="ribo_bam" type="data" format="BAM" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
         <param name="rna_bam" type="data" format="BAM" label="rna_bam" help="RNA-seq alignment file in BAM format."/>
-        <param name="read_lenghts_ribo1" type="text" value="26"  label="Read length 1" help="Read length 1, which is used for P-site calculation. Default is '26' but it varies a lot in different datasets. Please run 'ribotaper part 2' to deterimine a appropriate value."/>
-        <param name="read_lenghts_ribo2" type="text" value="28"  label="Read length 2" help="Read length 2, which is used for P-site calculation. Default is '28' but it varies a lot in different datasets.  Please run 'ribotaper part 2' to deterimine a appropriate value"/>
-        <param name="read_lenghts_ribo3" type="text" value="29"  label="Read length 3" help="Read length 3, which is used for P-site calculation. Default is '29' but it varies a lot in different datasets.  Please run 'ribotaper part 2' to deterimine a appropriate value"/>
-        <param name="cutoff1" type="text" value="9"  label="Cutoff 1" help="Offset 1, which is used for P-sites calculation. Default is '9' but it varies a lot in different datasets.
-        Please run 'ribotaper part 2' to deterimine a appropriate value."/>
-        <param name="cutoff2" type="text" value="12"  label="Cutoff 2" help="Offset 2, which is used for P-sites calculation. Default is '12' but it varies a lot in different datasets.
-         Please run 'ribotaper part 2' to deterimine a appropriate value."/>
-        <param name="cutoff3" type="text" value="12"  label="Cutoff 3" help="Offset 3, which is used for P-sites calculation. Default is '12' but it varies a lot in different datasets.
-         Please run 'ribotaper part 2' to deterimine a appropriate value."/>
+        <param name="read_lenghts_ribo" type="text" value="26,28,29"  label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
+        Please run 'ribotaper part 2' to deterimine appropriate values."/>
+        <param name="cutoff" type="text" value="9,12,12"  label="Cutoff" help="Cutoffs, comma-separated values, which are used for P-sites calculation. Example, 9,12,12.
+        Please run 'ribotaper part 2' to deterimine appropriate values."/>
     </inputs>
     <outputs>
         <data name="output1" type="data" format="pdf" from_work_dir="quality_check_plots.pdf" label="QC plots"/>
@@ -48,15 +43,9 @@
     </outputs>
     <tests>
         <test>
-            <param name="annotation_path" value="annotation_path.tgz" ftype="compressed_archive"/>
+            <param name="annotation_path" value="annotation_path.tgz" ftype="zip"/>
             <param name="ribo_bam" value="test_ribo.bam"/>
             <param name="rna_bam" value="test_rna.bam"/>
-            <param name="read_lenghts_ribo1" value="26"/>
-            <param name="read_lenghts_ribo2" value="28"/>
-            <param name="read_lenghts_ribo3" value="29"/>
-            <param name="cutoff1" value="9"/>
-            <param name="cutoff2" value="12"/>
-            <param name="cutoff3" value="12"/>
             <output name="output2" file="ORFs_genes_found"/>
         </test>
     </tests>
@@ -106,15 +95,6 @@
 **ORF categories (length/coverage)**:
 PDF file containing info about the number of ORFs found, together with their length and coverage per category/annotation.
 
-Important notes
-----------------
-
-  - We ran the RiboTaper analysis on an SGE cluster, using 7 cores and h_vmem 8G. For each dataset, the complete RiboTaper workflow (from the bam files to final results) took ~ 1 day.
-
-  - The current RiboTaper framework is not designed to identify and quantify ORFs on different transcripts. This means the transcript annotation is crucial.
-
-  - Be careful about using scaffolds, both in the genome and GTF files, which may slow the whole pipeline.
-
 ]]></help>
     <citations>
         <citation type="doi">10.1038/nmeth.3688</citation>