Mercurial > repos > blankenberg > naive_variant_caller

changeset 17:6be51647d31a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 3e2fca43a0b119b34befa5d7642a07682d1d77af"
author blankenberg
date Thu, 05 Dec 2019 12:23:12 -0500
parents 07e71cf6c8ef
children
files naive_variant_caller.xml tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample
diffstat 3 files changed, 51 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/naive_variant_caller.xml	Tue Apr 03 10:52:11 2018 -0400
+++ b/naive_variant_caller.xml	Thu Dec 05 12:23:12 2019 -0500
@@ -59,10 +59,25 @@
   <inputs>
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
-        <option value="cached">Locally cached</option>
+        <option value="cached_fasta_indexes" selected="True">Locally cached</option>
         <option value="history">History</option>
+        <option value="cached">Locally cached (deprecated source)</option>
       </param>
-      <when value="cached">
+      <when value="cached_fasta_indexes">
+        <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="fasta_indexes" metadata_name="dbkey" metadata_column="dbkey" 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="fasta_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="cached"> <!-- deprecated, uses older samtools data table -->
         <repeat name="input_bams" title="BAM file" min="1" >
             <param name="input_bam" type="data" format="bam" label="BAM file">
               <validator type="unspecified_build" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Dec 05 12:23:12 2019 -0500
@@ -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
--- a/tool_data_table_conf.xml.sample	Tue Apr 03 10:52:11 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Dec 05 12:23:12 2019 -0500
@@ -1,5 +1,10 @@
 <tables>
     <!-- Location of SAMTools indexes and other files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+    <!-- Deprecated Location of SAMTools indexes and other files -->
     <table name="sam_fa_indexes" comment_char="#">
         <columns>line_type, value, path</columns>
         <file path="tool-data/sam_fa_indices.loc" />