# HG changeset patch
# User yutaka-saito
# Date 1429450766 -32400
# Node ID 20930a8f700bd62d011995052c4a941b3741750f
# Parent  06f8460885ff41ca1065c21a03103ade72b40bf1
rename some files

diff -r 06f8460885ff -r 20930a8f700b bsf-call_wrapper.pl
--- a/bsf-call_wrapper.pl	Sun Apr 19 20:51:13 2015 +0900
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use warnings;
-
-use FindBin;
-
-print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
-
-my ($idx, $in) = ("", "");
-my $default_option = "-o bsf-call.out -W bsfwork";
-
-my $tooldir = shift(@ARGV);
-$tooldir = $FindBin::Bin;
-$ENV{PATH} = "$tooldir/bin:" . $ENV{PATH};
-my $reference_source = shift(@ARGV);
-my $read_end = shift(@ARGV);
-my $gslot = shift(@ARGV);
-#$idx = "$tooldir/data/chrX.sub.fa";
-
-if ($reference_source eq "indexed") {
-    $idx = shift(@ARGV);
-}
-elsif ($reference_source eq "history") {
-    my $own = shift(@ARGV);
-    $idx = "reference.fa";
-    &invoke_command("ln -s $own reference.fa");
-}
-else {
-    die "never reach here\n";
-}
-
-if ($read_end eq "single-end") {
-    $in = shift(@ARGV);
-    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
-}
-elsif ($read_end eq "paired-end") {
-    my $in1 = shift(@ARGV);
-    my $in2 = shift(@ARGV);
-    $in = $in1 . "," . $in2;
-    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
-}
-else {
-    die "never reach here\n";
-}
-
-sub invoke_command {
-    my ($command) = @_;
-    print "invoking: $command\n";
-    system($command);
-}
diff -r 06f8460885ff -r 20930a8f700b bsf-call_wrapper.xml
--- a/bsf-call_wrapper.xml	Sun Apr 19 20:51:13 2015 +0900
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<tool id="bsf-call" name="bsf-call" version="1.0.0">
-  <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
-<!--
-  <version_command></version_command>
--->
-
-  <requirements>
-    <requirement type="set_environment">TOOLDIR</requirement>
-  </requirements>
-
-  <command interpreter="perl">
-    bsf-call_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1} 
-
-    #if $reference.source=="indexed":
-      $reference.index.fields.path
-    #else if $reference.source=="history":
-      $reference.own_file
-    #else 
-
-    #end if
-
-    #if $read.end=="single-end"
-      $in 
-    #else if $read.end=="paired-end"
-      $in1 $in2
-    #else
-      
-    #end if
-  </command>
-
-  <inputs>
-    <conditional name="reference">
-      <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
-        <option value="indexed">Use a built-in genome index</option>
-        <option value="history">Use a genome from the history and build index</option>
-      </param>
-      <when value="indexed">
-        <param name="index" type="select" label="Select reference genome">
-          <options from_data_table="bsf-call_indexes">
-            <filter type="sort_by" column="2"/>
-            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
-      </when>
-    </conditional>
-
-    <conditional name="read">
-      <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
-        <option value="single-end">Single-end reads</option>
-        <option value="paired-end">Paired-end reads</option>
-      </param>
-      <when value="single-end">
-        <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
-      </when>
-      <when value="paired-end">
-        <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
-        <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
-      </when>
-    </conditional> 
-  </inputs>
-
-  <outputs>
-    <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
-    <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
-  </outputs>
-
-  <help>
-**bsf-call**
-
-Mapping bisulfite-seq reads and calling methylated cytosines
-
-------
-
-**Input format**
-
-Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file). 
-
-------
-
-**Output format**
-
-Output is a six-column tab-delimited file::
-
-  Col.| Description
-  ----+--------------------------------------
-  1   | chromosome label (e.g. chr1)
-  2   | genomic position (0-based)
-  3   | strand (+,-)
-  4   | mC context (CG, CHG, CHH)
-  5   | mC rate (float)
-  6   | read coverage
-
-------
-
-**Contact**
-
-Toutai Mituyama
-
-mituyama-toutai AT aist.go.jp
-  </help>
-
-  <citations>
-    <citation type="doi">10.1093/nar/gkt1373</citation>
-  </citations>
-
-</tool>
-
-<!--
-Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory. 
- \${GALAXY_SLOTS:-4} 
-
-Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime). 
--->
diff -r 06f8460885ff -r 20930a8f700b bsfcall_wrapper.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsfcall_wrapper.pl	Sun Apr 19 22:39:26 2015 +0900
@@ -0,0 +1,51 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
+
+my ($idx, $in) = ("", "");
+my $default_option = "-o bsf-call.out -W bsfwork";
+
+my $tooldir = shift(@ARGV);
+$tooldir = $FindBin::Bin;
+$ENV{PATH} = "$tooldir/bin:" . $ENV{PATH};
+my $reference_source = shift(@ARGV);
+my $read_end = shift(@ARGV);
+my $gslot = shift(@ARGV);
+#$idx = "$tooldir/data/chrX.sub.fa";
+
+if ($reference_source eq "indexed") {
+    $idx = shift(@ARGV);
+}
+elsif ($reference_source eq "history") {
+    my $own = shift(@ARGV);
+    $idx = "reference.fa";
+    &invoke_command("ln -s $own reference.fa");
+}
+else {
+    die "never reach here\n";
+}
+
+if ($read_end eq "single-end") {
+    $in = shift(@ARGV);
+    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
+}
+elsif ($read_end eq "paired-end") {
+    my $in1 = shift(@ARGV);
+    my $in2 = shift(@ARGV);
+    $in = $in1 . "," . $in2;
+    &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
+}
+else {
+    die "never reach here\n";
+}
+
+sub invoke_command {
+    my ($command) = @_;
+    print "invoking: $command\n";
+    system($command);
+}
diff -r 06f8460885ff -r 20930a8f700b bsfcall_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bsfcall_wrapper.xml	Sun Apr 19 22:39:26 2015 +0900
@@ -0,0 +1,116 @@
+<tool id="bsfcall" name="bsfcall" version="1.0.0">
+  <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
+<!--
+  <version_command></version_command>
+-->
+
+  <requirements>
+    <requirement type="set_environment">TOOLDIR</requirement>
+  </requirements>
+
+  <command interpreter="perl">
+    bsfcall_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1} 
+
+    #if $reference.source=="indexed":
+      $reference.index.fields.path
+    #else if $reference.source=="history":
+      $reference.own_file
+    #else 
+
+    #end if
+
+    #if $read.end=="single-end"
+      $in 
+    #else if $read.end=="paired-end"
+      $in1 $in2
+    #else
+      
+    #end if
+  </command>
+
+  <inputs>
+    <conditional name="reference">
+      <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in genome index</option>
+        <option value="history">Use a genome from the history and build index</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select reference genome">
+          <options from_data_table="bsfcall_indexes">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
+      </when>
+    </conditional>
+
+    <conditional name="read">
+      <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
+        <option value="single-end">Single-end reads</option>
+        <option value="paired-end">Paired-end reads</option>
+      </param>
+      <when value="single-end">
+        <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
+      </when>
+      <when value="paired-end">
+        <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
+        <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
+      </when>
+    </conditional> 
+  </inputs>
+
+  <outputs>
+    <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
+    <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
+  </outputs>
+
+  <help>
+**bsf-call**
+
+Mapping bisulfite-seq reads and calling methylated cytosines
+
+------
+
+**Input format**
+
+Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file). 
+
+------
+
+**Output format**
+
+Output is a six-column tab-delimited file::
+
+  Col.| Description
+  ----+--------------------------------------
+  1   | chromosome label (e.g. chr1)
+  2   | genomic position (0-based)
+  3   | strand (+,-)
+  4   | mC context (CG, CHG, CHH)
+  5   | mC rate (float)
+  6   | read coverage
+
+------
+
+**Contact**
+
+Toutai Mituyama
+
+mituyama-toutai AT aist.go.jp
+  </help>
+
+  <citations>
+    <citation type="doi">10.1093/nar/gkt1373</citation>
+  </citations>
+
+</tool>
+
+<!--
+Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory. 
+ \${GALAXY_SLOTS:-4} 
+
+Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime). 
+-->
diff -r 06f8460885ff -r 20930a8f700b tool-data/bsf-call_indexes.loc.sample
--- a/tool-data/bsf-call_indexes.loc.sample	Sun Apr 19 20:51:13 2015 +0900
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-hg19	hg19	hg19	/disk/reference/Bisulfighter/Homo_sapiens/UCSC/hg19/Sequence/BsfcallIndex/genome.fa
-test	test	test	/disk/reference/Bisulfighter/Homo_sapiens/UCSC/hg19/Sequence/BsfcallIndex/chrX.sub.fa
diff -r 06f8460885ff -r 20930a8f700b tool-data/bsfcall_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bsfcall_indexes.loc.sample	Sun Apr 19 22:39:26 2015 +0900
@@ -0,0 +1,2 @@
+hg19	hg19	hg19	/disk/reference/Bisulfighter/Homo_sapiens/UCSC/hg19/Sequence/BsfcallIndex/genome.fa
+test	test	test	/disk/reference/Bisulfighter/Homo_sapiens/UCSC/hg19/Sequence/BsfcallIndex/chrX.sub.fa
diff -r 06f8460885ff -r 20930a8f700b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sun Apr 19 20:51:13 2015 +0900
+++ b/tool_data_table_conf.xml.sample	Sun Apr 19 22:39:26 2015 +0900
@@ -1,6 +1,6 @@
 <tables>
-  <table name="bsf-call_indexes" comment_char="#">
+  <table name="bsfcall_indexes" comment_char="#">
     <columns>value, dbkey, name, path</columns>
-    <file path="tool-data/bsf-call_indexes.loc"/>
+    <file path="tool-data/bsfcall_indexes.loc"/>
   </table>
 </tables>