changeset 1:0f17ca98338e draft default tip

Uploaded

--- a/fpfilter.xml	Tue Jul 03 06:05:44 2018 -0400
+++ b/fpfilter.xml	Sat Sep 21 13:20:34 2019 -0400
@@ -3,6 +3,7 @@
   <requirements>
     <requirement type="package" version="0.8" >bam-readcount</requirement>
     <requirement type="package" >samtools</requirement>
+    <requirement type="package" version="1.0" >openssl</requirement>
   </requirements>
   <command>
 	perl  $__tool_directory__/fpfilter.pl
@@ -10,7 +11,15 @@
 	--bam-file ${bam}
 	--bam-index  ${bam.metadata.bam_index}
 	--sample ${sample}
-	--reference ${reference}
+
+
+         #if $reference_source.reference_source_selector == "history"
+         --reference $reference_source.reference
+        #end if
+        #if $reference_source.reference_source_selector == "cached"
+         --reference  $reference_source.ref_file.fields.path
+        #end if
+
 	--output ${output}
 	--min-read-pos ${min_read_pos}
 	--min-var-freq ${min_var_freq}
@@ -27,8 +36,24 @@
     <param name="vcf" format="vcf" type="data" label="VCF File" help="The input VCF file. Must have a GT field." />
     <param name="bam" format="bam" type="data" label="bam file" help="The BAM file of the sample you are filtering on. Typically the tumor." />
     <param name="sample" type="text" label="Sample" value="sample" help="The sample name of the sample you want to filter on in the VCF file." />
-    <param name="reference" format="fasta" type="data" label="Reference Genome" help="A fasta containing the reference sequence the BAM file was aligned to"/>
-
+      <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from history as reference</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="fpf_index">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No indexes are available" />
+                    </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="history">
+                <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
+            </when> 
+      </conditional>
     <param name="min_read_pos" type="float" value="0.10" label="Min Read Pos" help="Minimum average relative distance from start/end of read." />
     <param name="min_var_freq" type="float" value="0.05" label="Min Var Freq" help="Minimum variant allele frequency." />
     <param name="min_var_count" type="integer" value="4" label="Min Var Count" help="Minimum number of variant-supporting reads." />

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fpf_index.loc.sample	Sat Sep 21 13:20:34 2019 -0400
@@ -0,0 +1,34 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of fpfilter indexed sequences data files. You will need
+#to create these data files and then create a fpf_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fpf_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_path>
+#
+#So, for example, if you had phiX indexed stored in 
+#/depot/data2/galaxy/phiX/base/, 
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.dict, phiX.fa.fai files.
+#
+#
+#Your fpf_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files.  For example:
+#
+#phiX174                                phiX    phiX174                 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon                              hg18    hg18 Canonical  /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full                               hg18    hg18 Full               /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa             hg19    hg19                    /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sat Sep 21 13:20:34 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in the fpfilter mapper format -->
+    <table name="fpf_index" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fpf_index.loc" />
+    </table>
+</tables>