# HG changeset patch
# User bgruening
# Date 1474193157 14400
# Node ID 03c74355227f2f8eab5e2a0913a072c04e40913c
# Parent  85d0d479f05b71a59a2a0114a3b635a5eda528fb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit edee3afc7d729be9a224d21729bb7490a3761a0e

diff -r 85d0d479f05b -r 03c74355227f sailfish.xml
--- a/sailfish.xml	Mon Dec 21 18:18:03 2015 -0500
+++ b/sailfish.xml	Sun Sep 18 06:05:57 2016 -0400
@@ -1,7 +1,8 @@
-<tool id="sailfish" name="Sailfish" version="0.7.6.0">
+<tool id="sailfish" name="Sailfish" version="0.7.6.1">
     <description>transcript quantification from RNA-seq data</description>
     <requirements>
         <requirement type="package" version="0.7.6">sailfish</requirement>
+        <requirement type="package" version="1.57.0">boost</requirement>
     </requirements>
     <macros>
         <xml name="strandedness">
@@ -72,7 +73,7 @@
                 --mates2 ./mate2.$ext
                 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
             #end if
-            --output ./ 
+            --output ./
             $biasCorrect
             --threads "\${GALAXY_SLOTS:-4}"
 
@@ -117,9 +118,9 @@
                 </param>
             </when>  <!-- build-in -->
             <when value="history">
-                <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" />
+                <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" help="in FASTA format" />
                 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built"
-                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. 
+                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
                         The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers,
                         the more distinct they will be.  We generally recommend using a k-mer size of at least 20."/>
             </when>  <!-- history -->
@@ -208,6 +209,7 @@
     </tests>
     <help>
 <![CDATA[
+
 **What it does**
 
 Sailfish is a tool for transcript quantification from RNA-seq data.  It
@@ -310,18 +312,18 @@
     OSR (a stranded paired-end protocol where the reads face away from each other,
          read1 comes from reverse strand and read2 comes from the forward strand)
 
-.. note:: Correspondence to TopHat library types 
+.. note:: Correspondence to TopHat library types
 
-   The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq 
+   The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
    read aligner has a different convention for specifying the format of the library.
    Below is a table that provides the corresponding sailfish/salmon library format
    string for each of the potential TopHat library types:
 
 
-   +---------------------+-------------------------+  
+   +---------------------+-------------------------+
    | TopHat              | Salmon (and Sailfish)   |
    +=====================+============+============+
-   |                     | Paired-end | Single-end | 
+   |                     | Paired-end | Single-end |
    +---------------------+------------+------------+
    |``-fr-unstranded``   |``-l IU``   |``-l U``    |
    +---------------------+------------+------------+
diff -r 85d0d479f05b -r 03c74355227f tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 21 18:18:03 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="sailfish" version="0.7.6">
-        <repository changeset_revision="04996d8b8587" name="package_sailfish_0_7_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>