Mercurial > repos > devteam > samtools_mpileup

changeset 1:b47a418ccfdc draft

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Uploaded tarball for 0.0.2 version on main tool shed.
author devteam
date Wed, 12 Mar 2014 12:52:52 -0400
parents f8ea7725e333
children 3aa48bcbc599
files samtools_mpileup.xml tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 4 files changed, 47 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_mpileup.xml	Tue Aug 20 12:34:40 2013 -0400
+++ b/samtools_mpileup.xml	Wed Mar 12 12:52:52 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_mpileup" name="MPileup" version="0.0.1">
+<tool id="samtools_mpileup" name="MPileup" version="0.0.2">
   <description>SNP and indel caller</description>
   <requirements>
       <requirement type="package" version="0.1.18">samtools</requirement>
@@ -59,22 +59,22 @@
       </param>
       <when value="cached">
         <repeat name="input_bams" title="BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
-            </param>
+          <param name="input_bam" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+          </param>
         </repeat>
         <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="sam_fa_indexes">
-            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
+          <options from_data_table="fasta_indexes">
+            <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...-->
           </options>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <repeat name="input_bams" title="BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file" >
-              <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
-            </param>
+          <param name="input_bam" type="data" format="bam" label="BAM file">
+            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." />
+          </param>
         </repeat>
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed Mar 12 12:52:52 2014 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Mar 12 12:52:52 2014 -0400
@@ -0,0 +1,7 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
--- a/tool_dependencies.xml	Tue Aug 20 12:34:40 2013 -0400
+++ b/tool_dependencies.xml	Wed Mar 12 12:52:52 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>