# HG changeset patch
# User pitagora <ryota.yamanaka@riken.jp>
# Date 1427343514 -32400
# Node ID 0283d2d3f8d6e4a6854d03947fe85331468ef139
# Parent  05154d5ffbdbb4454addce4e540eb343b6d10c60
commit

diff -r 05154d5ffbdb -r 0283d2d3f8d6 README.rst
--- a/README.rst	Thu Mar 26 13:15:17 2015 +0900
+++ b/README.rst	Thu Mar 26 13:18:34 2015 +0900
@@ -1,53 +1,9 @@
-Galaxy wrappers for sailfish
-=====================================
-
-These wrappers are copyright 2014 by Björn Grüning and additional contributors. 
-All rights reserved. See the licence text below.
-
-Currently tested with sailfish 0.6.3.
-
-
-Automated Installation
-======================
+This code is originated from the followings. Prease refer them for the licence information:
 
-Galaxy should be able to automatically install the sailfish for you.
-
-
-History
-=======
-
-======== ======================================================================
-Version  Changes
--------- ----------------------------------------------------------------------
-v0.6.3.0  - First release
-
-======== ======================================================================
-
+Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish
 
-Bug Reports
-===========
-
-You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
-us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
-
-
-Licence (MIT)
-=============
+Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+If you use this Galaxy tool in work leading to a scientific publication please cite the following:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/
diff -r 05154d5ffbdb -r 0283d2d3f8d6 sailfish.xml
--- a/sailfish.xml	Thu Mar 26 13:15:17 2015 +0900
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-<tool id="sailfish" name="Sailfish" version="0.6.3.0">
-    <description>transcript quantification from RNA-seq data</description>
-    <version_command>sailfish -version</version_command>
-    <expand macro="requirements" />
-    <command>
-<![CDATA[
-        sailfish quant -i $index_dir 
-            #if $single_or_paired-single_or_paired_opts == 'single':
-                -l "TYPE=SE"
-                -r $single_or_paired_opts.input_singles
-            #else:
-                -1 $single_or_paired_opts.input_mate1
-                -2 $single_or_paired_opts.input_mate2
-                #if $single_or_paired_opts.orientation == "same":
-                    -l "TYPE=PE:O=>>"
-                #elif $single_or_paired_opts.orientation == "away":
-                    -l "TYPE=PE:O=<>"
-                #else:
-                    -l "TYPE=PE:O=><"
-                #end if
-            #end if
--o <quant_dir>
-
-]]>
-    </command>
-    <expand macro="stdio" />
-    <inputs>
-        <conditional name="single_or_paired">
-            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
-              <option value="single">Single-end</option>
-              <option value="paired">Paired-end</option>
-            </param>
-            <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
-            </when>
-            <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." />
-                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
-                    <option value="same">Mates are oriented in the same direction</option>
-                    <option value="away">Mates are oriented away from each other</option>
-                    <option value="toward" selected="True">Mates are oriented toward each other</option>
-                </param>
-            </when>
-        </conditional>
-
-        <expand macro="input_conditional_index" />
-
-    </inputs>
-    <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
-            <expand macro="output_change_format" />
-        </data>
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-<![CDATA[
-**What it does**
-
-
-The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is 
-upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa.
-
-The second option &lt;&gt; denotes that the mates are oriented away from each other. This implies that start 
-of mate1 is closer to start of mate 2 than the end of mate 2, etc.
-
-The third option &gt;&lt; is, perhaps, the most common relative orientation. It denotes that the mates are 
-oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa.
-
--------
-
-**References**
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite the following:
-
-
-]]>
-    </help>
-</tool>
diff -r 05154d5ffbdb -r 0283d2d3f8d6 sailfish_linux.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sailfish_linux.xml	Thu Mar 26 13:18:34 2015 +0900
@@ -0,0 +1,117 @@
+
+<tool id="sailfish_linux" name="Sailfish" version="0.6.3">
+    <description>transcript quantification from RNA-seq data</description>
+    <version_command>sailfish -version</version_command>
+    <!-- <expand macro="requirements" /> -->
+    <requirements>
+        <requirement type="package" version="0.6.3">sailfish_linux</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        sailfish quant -i ${filter(lambda x: str(x[0]) == str($index_path), $__app__.tool_data_tables['sailfish_custom_indexes'].get_fields())[0][-1]}
+            #if $single_or_paired.single_or_paired_opts == 'single':
+                -l "T=SE"
+                -r $single_or_paired.input_singles
+            #else:
+                #if $single_or_paired.orientation == "same":
+                    #if $single_or_paired.strandedness == "sense":
+                        -l "T=PE:O=>>:S=S"
+                    #elif $single_or_paired.strandedness == "antisense":
+                        -l "T=PE:O=>>:S=A"
+                    #else:
+                        -l "T=PE:O=>>:S=U"
+                    #end if
+                #elif $single_or_paired.orientation == "away":
+                    #if $single_or_paired.strandedness == "sense":
+                        -l "T=PE:O=<>:S=S"
+                    #elif $single_or_paired.strandedness == "antisense":
+                        -l "T=PE:O=<>:S=A"
+                    #else:
+                        -l "T=PE:O=<>:S=U"
+                    #end if
+                #else:
+                    #if $single_or_paired.strandedness == "sense":
+                        -l "T=PE:O=><:S=S"
+                    #elif $single_or_paired.strandedness == "antisense":
+                        -l "T=PE:O=><:S=A"
+                    #else:
+                        -l "T=PE:O=><:S=U"
+                    #end if
+                #end if
+                -1 $single_or_paired.input_mate1
+                -2 $single_or_paired.input_mate2
+            #end if
+         -o ./ >> $log 2>&1
+]]>
+    </command>
+    <!-- <expand macro="stdio" /> -->
+    <inputs>
+        <param name="index_path" type="select" label="Select a sailfish index">
+            <options from_data_table="sailfish_custom_indexes">
+                <validator type="no_options" message="No index are available"/>
+            </options>
+        </param>
+        <conditional name="single_or_paired">
+            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." />
+                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
+                    <option value="same">Mates are oriented in the same direction</option>
+                    <option value="away">Mates are oriented away from each other</option>
+                    <option value="toward" selected="True">Mates are oriented toward each other</option>
+                </param>
+                <param name="strandedness" type="select" label="Specifies the strandedness of the reads">
+                    <option value="sense">sense strand</option>
+                    <option value="antisense">antisense strand</option>
+                    <option value="unknown" selected="True">unknown strandedness</option>
+                </param>
+            </when>
+        </conditional>
+        <!-- <expand macro="input_conditional_index" /> -->
+    </inputs>
+    <outputs>
+        <data name="log"   format="txt" label="${tool.name} on ${on_string}: log"/>
+        <data name="quant" format="txt" from_work_dir="quant.sf" label="${tool.name} on ${on_string}: quant"/>
+        <data name="quant_bias_corrected" format="txt" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string}: quant_bias_corrected"/>
+        <data name="reads_count_info" format="txt" from_work_dir="reads.count_info" label="${tool.name} on ${on_string}: reads_count_info"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is 
+upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa.
+
+The second option &lt;&gt; denotes that the mates are oriented away from each other. This implies that start 
+of mate1 is closer to start of mate 2 than the end of mate 2, etc.
+
+The third option &gt;&lt; is, perhaps, the most common relative orientation. It denotes that the mates are 
+oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa.
+
+-------
+
+**References**
+
+This code is originated from the followings. Prease refer them for the licence information:
+
+Mika Yoshimura's code: https://github.com/myoshimura080822/galaxy-mytools_sailfish
+
+Björn Grüning's code: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish
+
+If you use this Galaxy tool in work leading to a scientific publication please cite the following:
+
+Sailfish: http://www.cs.cmu.edu/~ckingsf/software/sailfish/
+
+]]>
+    </help>
+</tool>
+
diff -r 05154d5ffbdb -r 0283d2d3f8d6 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 26 13:15:17 2015 +0900
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="sailfish" version="0.6.3">
-        <repository changeset_revision="6453a4f36990" name="package_sailfish_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r 05154d5ffbdb -r 0283d2d3f8d6 tool_dependency.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependency.xml	Thu Mar 26 13:18:34 2015 +0900
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="sailfish_linux" version="0.6.3">
+    <repository changeset_revision="2c66da813a79" name="package_sailfish_linux_0_6_3" owner="pitagora" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  </package>
+</tool_dependency>