Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

changeset 2:b2eb07000039

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Fix spacing in environment_variables in tool_dependencies (breaks env.sh) Cleanup help sections.
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 15:40:22 +0100
parents 4419c2f77b60
children d7ce95ccf54f 423ad61697c4
files metagene.xml prepare.xml tool_dependencies.xml triplet.xml
diffstat 4 files changed, 37 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/metagene.xml	Tue Jul 21 14:58:34 2015 +0100
+++ b/metagene.xml	Tue Jul 21 15:40:22 2015 +0100
@@ -148,18 +148,18 @@
 #. Select *Triplet periodicity (R data file)* from the previous step.
 
 #. Specify length of ribosome footprint reads to be used in filtering
-(lengths). Only these reads **will** be used in the analysis.
+   (lengths). Only these reads **will** be used in the analysis.
 
 #. Specify frames to consider. This information can be obtained
-from the *Triplet periodicity (HTML report)*.
+   from the *Triplet periodicity (HTML report)*.
 
-.. class:: warningmark
+   .. class:: warningmark
 
-Please note that the frames specified should correspond to the
-lengths of the reads.
+       Please note that the frames specified should correspond to the
+       lengths of the reads.
 
 #. Under *plotCDS parameters*, input length of footprints to be considered for
-generating the plot.
+   generating the plot.
 
 #. Review/change other options if necessary and execute program.
 
@@ -169,12 +169,12 @@
 
 #. Metagene analysis (HTML report)
 
-A HTML file with results and links to other output files - plots for
-specified lengths (PDF) and R script used for the session.
+   A HTML file with results and links to other output files - plots for
+   specified lengths (PDF) and R script used for the session.
 
 #. Metagene analysis (R data file)
 
-Used as input for the next step - *Plot Rribosome Profile*.
+   Used as input for the next step - *Plot Rribosome Profile*.
 
 riboSeqR functions used
 .......................
--- a/prepare.xml	Tue Jul 21 14:58:34 2015 +0100
+++ b/prepare.xml	Tue Jul 21 15:40:22 2015 +0100
@@ -105,12 +105,12 @@
 
 This tool can be used to prepare input data for riboSeqR from SAM
 format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
-do this alignment manually using bowtie or the
+do this alignment manually using bowtie or using the
 "Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
 tool on `RiboGalaxy &lt;http://ribogalaxy.ucc.ie&gt;`_.
 
 The required input format for riboSeqR is mentioned in the
-*"Getting Data"* section of the documentation.
+"Getting Data" section of the documentation.
 
 How to use?
 -----------
@@ -126,28 +126,34 @@
 The following files will be generated on completion:
 
 #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
-output files.
+   output files.
+
+#. Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
+   These files are plain text and lines have the following information -
+   strand, transcript name, alignment position, sequence.
 
-* Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
-These files are plain text and lines have the following information -
-strand, transcript name, alignment position, sequence.
+   .. class:: infomark
 
-Please note the alignments are made *0-indexed*.
+        Please note the alignments are made **0-indexed**. Additional information on
+        how the SAM alignments are processed can be found below.
 
-* R script used in this session.
+#. R script used in this session.
 
 #. Prepare riboSeqR input (R data file) - used as input for the next step -
-*Triplet Periodicity*.
+   *Triplet Periodicity*.
 
 How are the SAM alignments processed?
 .....................................
 #. Lines starting with ``@`` are ignored.
+
 #. Lines having a ``FLAG=0`` are considered as successful alignments. These are
-considered for the next step.
+   considered for the next step.
+
 #. Alignment start is located on ``column 4``. These are decremented by
-1 as SAM alignments are 1-indexed.
+   1 as SAM alignments are 1-indexed.
+
 #. riboSeqR input file is written with the strand (``+``), transcript name,
-alignment start and the aligned sequence.
+   alignment start and the aligned sequence.
 
 riboSeqR functions used
 .......................
--- a/tool_dependencies.xml	Tue Jul 21 14:58:34 2015 +0100
+++ b/tool_dependencies.xml	Tue Jul 21 15:40:22 2015 +0100
@@ -33,18 +33,10 @@
                     python setup.py build --r-home $R_HOME --r-home-lib $R_HOME/lib install --install-lib $INSTALL_DIR/lib/python
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">
-                        $INSTALL_DIR/lib/python
-                    </environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">
-                        $ENV[READLINE_LIB_PATH]
-                    </environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">
-                        $ENV[RHOME]/lib
-                    </environment_variable>
-                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">
-                        $ENV[R_ROOT_DIR]/lib
-                    </environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[READLINE_LIB_PATH]</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[RHOME]/lib</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[R_ROOT_DIR]/lib</environment_variable>
                 </action>
             </actions>
         </install>
--- a/triplet.xml	Tue Jul 21 14:58:34 2015 +0100
+++ b/triplet.xml	Tue Jul 21 15:40:22 2015 +0100
@@ -108,10 +108,10 @@
 #. Prepare riboSeqR input (R data file) from the previous step.
 #. FASTA format file of the reference transcriptome.
 
-.. class:: infomark
+   .. class:: infomark
 
-Please note that the FASTA header of the transcriptome sequences must
-match the sequence names from the SAM file.
+        Please note that the FASTA header of the transcriptome sequences must
+        match the sequence names from the SAM file.
 
 How to use?
 -----------
@@ -128,12 +128,12 @@
 
 #. Triplet periodicity (HTML report)
 
-A HTML file with results and links to other output files - triplet
-periodicity plot (PDF) and R script used for the session.
+   A HTML file with results and links to other output files - triplet
+   periodicity plot (PDF) and R script used for the session.
 
 #. Triplet periodicity (R data file)
 
-Used as input for the next step - *Metagene analysis*.
+   Used as input for the next step - *Metagene analysis*.
 
 riboSeqR functions used
 .......................