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Merge
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents 423ad61697c4 (current diff) de357bab306d (diff)
children
files README.rst test-data/Prepare riboSeqR input (R data file)
diffstat 7 files changed, 231 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/.hgignore	Tue Oct 27 12:21:50 2015 +0000
+++ b/.hgignore	Tue Oct 27 12:29:39 2015 +0000
@@ -1,3 +1,4 @@
 syntax: glob
 
+.git*
 *.pyc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-riboSeqR_chlamydomonas_test_data.ga	Tue Oct 27 12:29:39 2015 +0000
@@ -0,0 +1,155 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "riboSeqR chlamydomonas test data", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 10, 
+                "top": 10
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "rdata_load": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Triplet Periodicity", 
+            "outputs": [
+                {
+                    "name": "rdata_save", 
+                    "type": "rda"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 230, 
+                "top": 10
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_triplet_periodicity/0.4.0", 
+            "tool_state": "{\"__page__\": 0, \"analyze_plot_lengths\": \"\\\"26:30\\\"\", \"include_lengths\": \"\\\"25:30\\\"\", \"fasta_file\": \"null\", \"stop_codons\": \"\\\"TAG, TAA, TGA\\\"\", \"start_codons\": \"\\\"ATG\\\"\", \"rdata_load\": \"null\", \"text_legend\": \"\\\"Frame 0, Frame 1, Frame 2\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": null, 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "rdata_load": {
+                    "id": 1, 
+                    "output_name": "rdata_save"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Metagene Analysis", 
+            "outputs": [
+                {
+                    "name": "rdata_save", 
+                    "type": "rda"
+                }, 
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 450, 
+                "top": 10
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_metagene/0.4.0", 
+            "tool_state": "{\"__page__\": 0, \"rdata_load\": \"null\", \"unique_hit_mean\": \"\\\"10\\\"\", \"min3p\": \"\\\"-200\\\"\", \"__rerun_remap_job_id__\": null, \"cap\": \"\\\"\\\"\", \"ratio_check\": \"\\\"True\\\"\", \"max3p\": \"\\\"20\\\"\", \"plot_lengths\": \"\\\"27,28\\\"\", \"max5p\": \"\\\"200\\\"\", \"selected_lengths\": \"\\\"27,28\\\"\", \"plot_title\": \"\\\"\\\"\", \"hit_mean\": \"\\\"50\\\"\", \"selected_frames\": \"\\\"1,0\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"min5p\": \"\\\"-20\\\"\"}", 
+            "tool_version": null, 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "rdata_load": {
+                    "id": 2, 
+                    "output_name": "rdata_save"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Plot Ribosome Profile", 
+            "outputs": [
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 670, 
+                "top": 10
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/riboseqr_ribosome_profile/0.4.0", 
+            "tool_state": "{\"__page__\": 0, \"transcript_cap\": \"\\\"200\\\"\", \"__rerun_remap_job_id__\": null, \"transcript_length\": \"\\\"27\\\"\", \"rdata_load\": \"null\", \"transcript_name\": \"\\\"CUFF.37930.1\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": null, 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "rdata_load": {
+                    "id": 2, 
+                    "output_name": "rdata_save"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Differential Translation Analysis", 
+            "outputs": [
+                {
+                    "name": "html_file", 
+                    "type": "html"
+                }
+            ], 
+            "position": {
+                "left": 670, 
+                "top": 130
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/vimalkumarvelayudhan/riboseqr_wrapper/difftrans/0.1.0", 
+            "tool_state": "{\"normalize\": \"\\\"True\\\"\", \"__page__\": 0, \"num_counts\": \"\\\"10\\\"\", \"__rerun_remap_job_id__\": null, \"rdata_load\": \"null\", \"group1\": \"\\\"1,1,1,1\\\"\", \"frames_type\": \"{\\\"select_frames\\\": \\\"each\\\", \\\"frames_each\\\": \\\"0,2\\\", \\\"__current_case__\\\": 1}\", \"group2\": \"\\\"WT,WT,M,M\\\"\", \"frames\": \"\\\"0,2\\\"\", \"slice_lengths\": \"\\\"27,28\\\"\", \"chromInfo\": \"\\\"/mnt/workspace/DATA/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": null, 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
--- a/README.rst	Tue Oct 27 12:21:50 2015 +0000
+++ b/README.rst	Tue Oct 27 12:29:39 2015 +0000
@@ -1,22 +1,13 @@
-README
-------
-
+riboseqr_wrapper
+================
 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
-integration for `Galaxy <http://galaxyproject.org/>`_ /
-`RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
+integration for `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_ and `Galaxy <http://galaxyproject.org/>`_.
 
 Included tools
-..............
-In the order in which they are run
-
-#. Prepare riboSeqR Input
+--------------
+In the order they are run
 
-   Prepare riboSeqR format input files from alignment files (SAM format,
-   Ribo-Seq or RNA-Seq alignments).
-
-#. Triplet Periodicity
-
-   Plot triplet periodicity for different read lengths.
+#. Plot triplet periodicity for different read lengths.
 
 #. Metagene Analysis
 
@@ -33,12 +24,52 @@
    Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
    translation analysis with baySeq.
 
-Tested with
-...........
-**R** ``3.1.2``
+Dependencies
+------------
+Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
+
+R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
+
+How to test
+-----------
+1. Upload the following test data files from the test-data folder.
+
+   Prepare riboSeqR input (R data file)
+
+   rsem_chlamy236_deNovo.transcripts.fa
+
+2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
+   can currently be tested using this workflow. Import this workflow into Galaxy.
+
+3. Run workflow
+
+   In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
+
+   In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
+
+   Run workflow.
 
-**riboSeqR** ``1.0.5``
+
+About the test data files
+.........................
+The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
+riboSeqR package. The commands used were ::
+
+   library(riboSeqR)
+
+   datadir <- system.file("extdata", package = "riboSeqR")
+   chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
 
-**baySeq** ``2.0.50``
+   fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
+
+   ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
+   rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
 
-**rpy2** ``2.3.10``
+   riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
+   save(riboDat, file="Prepare riboSeqR input (R data file)")
+
+rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
+
+Bugs/Issues?
+------------
+Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues
--- a/difftrans.xml	Tue Oct 27 12:21:50 2015 +0000
+++ b/difftrans.xml	Tue Oct 27 12:29:39 2015 +0000
@@ -25,7 +25,7 @@
         --output_path "$html_file.files_path"
     </command>
     <inputs>
-        <param name="rdata_load" format="rda" type="data"
+        <param name="rdata_load" format="RData" type="data"
                label="Select Metagene analysis (R data file)"
                multiple="false">
             <validator type="expression"
@@ -61,7 +61,7 @@
     </outputs>
     <!--<tests>-->
     <!--<test>-->
-    <!--<param name="rdata_load" value="Metagene analysis (R data file)"/>-->
+    <!--<param name="rdata_load" value="Metagene analysis (R data file)" ftype="RData" />-->
     <!--<param name="slice_lengths" value="27,28"/>-->
     <!--<param name="frames" value="0,2"/>-->
     <!--<param name="group1" value="1,1,1,1"/>-->
--- a/metagene.xml	Tue Oct 27 12:21:50 2015 +0000
+++ b/metagene.xml	Tue Oct 27 12:29:39 2015 +0000
@@ -27,7 +27,7 @@
         --output_path "$html_file.files_path"
     </command>
     <inputs>
-        <param name="rdata_load" type="data" format="rda"
+        <param name="rdata_load" type="data" format="RData"
                label="Select Triplet periodicity (R data file)"
                multiple="false" optional="false"
                help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;filterHits parameters (footprint reads to be used in the analysis)&lt;/font&gt;&lt;/h4&gt;">
@@ -103,14 +103,14 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
     <outputs>
-        <data format="rda" name="rdata_save"
+        <data format="RData" name="rdata_save"
               label="Metagene analysis (R data file)"/>
         <data format="html" name="html_file"
               label="Metagene analysis (HTML report)"/>
     </outputs>
     <!--<tests>-->
     <!--<test>-->
-    <!--<param name="rdata_load" value="Triplet periodicity (R data file)" ftype="rda"/>-->
+    <!--<param name="rdata_load" value="Triplet periodicity (R data file)" ftype="RData"/>-->
     <!--<param name="hit_mean" value="50"/>-->
     <!--<param name="unique_hit_mean" value="10"/>-->
     <!--<param name="min5p" value="-20"/>-->
@@ -119,7 +119,7 @@
     <!--<param name="max3p" value="20"/>-->
     <!--<param name="cap" value=""/>-->
     <!--<param name="plot_title" value=""/>-->
-    <!--<output name="rdata_save" file="Metagene analysis (R data file)" ftype="rda"/>-->
+    <!--<output name="rdata_save" file="Metagene analysis (R data file)" ftype="RData"/>-->
     <!--<output name="html_file" file="Metagene_analysis_(HTML_report).html">-->
     <!--<extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>-->
     <!--<extra_files type="file" name="Metagene-analysis-plot1_1.png" value="Metagene-analysis-plot1_1.png"/>-->
--- a/ribosome_profile.xml	Tue Oct 27 12:21:50 2015 +0000
+++ b/ribosome_profile.xml	Tue Oct 27 12:29:39 2015 +0000
@@ -21,7 +21,7 @@
         --output_path "$html_file.files_path"
     </command>
     <inputs>
-        <param name="rdata_load" format="rda" type="data"
+        <param name="rdata_load" format="RData" type="data"
                label="Select Metagene analysis (R data file)"
                multiple="false">
             <validator type="expression"
@@ -59,7 +59,7 @@
     </outputs>
     <!--<tests>-->
         <!--<test>-->
-            <!--<param name="rdata_load" value="Metagene analysis (R data file)"/>-->
+            <!--<param name="rdata_load" value="Metagene analysis (R data file)" ftype="RData" />-->
             <!--<param name="transcript_name" value="CUFF.37930.1"/>-->
             <!--<param name="transcript_length" value="27"/>-->
             <!--<param name="transcript_cap" value="200"/>-->
--- a/triplet.xml	Tue Oct 27 12:21:50 2015 +0000
+++ b/triplet.xml	Tue Oct 27 12:29:39 2015 +0000
@@ -25,7 +25,7 @@
         --output_path "$html_file.files_path"
     </command>
     <inputs>
-        <param name="rdata_load" type="data" format="rda"
+        <param name="rdata_load" type="data" format="RData"
                label="Select prepared riboSeqR input (R data file)"
                multiple="false" optional="false"
                help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;findCDS
@@ -79,24 +79,24 @@
                       plot" help="Comma-separated values."/>
     </inputs>
     <outputs>
-        <data format="rda" name="rdata_save"
+        <data format="RData" name="rdata_save"
               label="Triplet periodicity (R data file)"/>
         <data format="html" name="html_file"
               label="Triplet periodicity (HTML report)"/>
     </outputs>
-    <tests>
-        <test>
-            <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda" />
-            <param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />
-            <param name="include_lengths" value="25:30" />
-            <param name="analyze_plot_lengths" value="26:30" />
-            <output name="rdata_save" file="Triplet periodicity (R data file)" ftype="rda" />
-            <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
-                <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />
-                <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />
-            </output>
-        </test>
-    </tests>
+    <!--<tests>-->
+        <!--<test>-->
+            <!--<param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="RData" />-->
+            <!--<param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />-->
+            <!--<param name="include_lengths" value="25:30" />-->
+            <!--<param name="analyze_plot_lengths" value="26:30" />-->
+            <!--<output name="rdata_save" file="Triplet periodicity (R data file)" ftype="RData" />-->
+            <!--<output name="html_file" file="Triplet_periodicity_(HTML_report).html">-->
+                <!--<extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />-->
+                <!--<extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />-->
+            <!--</output>-->
+        <!--</test>-->
+    <!--</tests>-->
     <help>
 Triplet Periodicity
 -------------------