diff docs/usage.rst @ 14:628f82e72d72

Version as released on PyPI 0.1.0

--- a/docs/usage.rst	Fri Aug 21 12:37:54 2015 +0100
+++ b/docs/usage.rst	Wed Aug 26 16:37:10 2015 +0100
@@ -10,57 +10,60 @@
 
 Parameters
 ..........
-1. Ribo-Seq alignment file (Sorted BAM file)
 
-   A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
-   file should be sorted. This can be done using one of the following methods.
+1. Ribo-Seq alignment file (Sorted BAM file)
+++++++++++++++++++++++++++++++++++++++++++++
+A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
+file should be sorted. This can be done using one of the following methods.
 
-   1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
-   2. ``samtools sort input.bam inputsorted``
+1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset.
+2. ``samtools sort input.bam inputsorted``
 
 2. Transcriptome (FASTA)
-
-   A FASTA format file with sequences of the transcripts.
+++++++++++++++++++++++++
+A FASTA format file with sequences of the transcripts.
 
 3. Name of the transcript to plot (Text)
-
-   The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
-   and the Ribo-Seq/RNA-Seq alignment (BAM).
+++++++++++++++++++++++++++++++++++++++++
+The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
+and the Ribo-Seq/RNA-Seq alignment (BAM).
 
 4. RNA coverage [optional] (Sorted BAM file)
-
-   If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
+++++++++++++++++++++++++++++++++++++++++++++
+If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
 
 5. Read lengths to consider [Optional] (Integer - 0 or greater)
-
-   If this option is provided, only Ribo-Seq data of the given length is considered.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+If this option is provided, only Ribo-Seq data of the given length is considered.
 
 6. Offset [optional] (Integer - 0 or greater)
-
-   If this option is provided, this offset is added to the read alignment positions.
++++++++++++++++++++++++++++++++++++++++++++++
+If this option is provided, this offset is added to the read alignment positions.
 
 Output
 ......
 1. Plots (PNG and SVG)
+++++++++++++++++++++++
+Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
 
-   Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
+RNA coverage as a gray background (if the RNA coverage option was selected).
 
-   RNA coverage as a gray background (if the RNA coverage option was selected).
+The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
 
-   The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
+The color codes are start (white) and stop (dark gray).
 
-   The color codes are start (white) and stop (dark gray).
+.. image:: ../images/riboplot.png
 
-   .. image:: ../images/riboplot.png
-
-2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
+2. RiboSeq read counts (CSV)
+++++++++++++++++++++++++++++
+In 3 frames for each position in the transcript.
 
 
 Command line
 ............
 ``riboplot`` can also be run on the command line. The usage is ::
 
-    usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
+    usage: riboplot [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
                     [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
                     [-o OUTPUT_PATH] [-d]
 
@@ -105,29 +108,29 @@
 Parameters
 ..........
 1. Ribo-Seq alignment file (Sorted BAM file)
+++++++++++++++++++++++++++++++++++++++++++++
+A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
+file should be sorted. This can be done using one of the following methods.
 
-   A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
-   file should be sorted. This can be done using one of the following methods.
-
-   1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
-   2. ``samtools sort input.bam inputsorted``
+1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset.
+2. ``samtools sort input.bam inputsorted``
 
 2. Transcriptome (FASTA)
-
-   A FASTA format file with sequences of the transcripts.
+++++++++++++++++++++++++
+A FASTA format file with sequences of the transcripts.
 
 3. Read lengths to consider [optional] (Integer - 0 or greater)
-
-   If this option is provided, only Ribo-Seq data of the given length is considered.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+If this option is provided, only Ribo-Seq data of the given length is considered.
 
 4. Offset [optional] (Integer - 0 or greater)
-
-   If this option is provided, this offset is added to the read alignment positions.
++++++++++++++++++++++++++++++++++++++++++++++
+If this option is provided, this offset is added to the read alignment positions.
 
 Output
 ......
 Read counts for all transcripts in the alignment (ZIP)
-
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
 
@@ -140,7 +143,7 @@
 ............
 ``ribocount`` can also be run on the command line. The usage is ::
 
-    usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
+    usage: ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
     [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
 
     Output read counts for all transcripts
@@ -172,3 +175,6 @@
         -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
             FASTA format file of the transcriptome
 
+.. links
+.. _RiboGalaxy: http://ribogalaxy.ucc.ie
+