changeset 3:4bf7233a372b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Thu Oct 04 10:26:01 2018 -0400
@@ -0,0 +1,11 @@
+name: affy2vcf
+owner: greg
+description: |
+  Contains a tool that converts Affymetrix genotype calls and intensity files to VCF format.
+homepage_url: https://github.com/freeseek/gtc2vcf
+long_description: |
+  Contains a tool that converts Affymetrix genotype calls and intensity files to VCF format.
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/convert_formats/affy2vcf
+type: unrestricted
+categories:
+  - Convert Formats

--- a/affy2vcf.xml	Thu Oct 04 10:16:02 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-<tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
-    <description>genotype calls and intensities to VCF</description>
-    <requirements>
-        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-#set text_outputs_dir = 'text_outputs'
-mkdir $text_outputs_dir &&
-bcftools +affy2vcf.so
--- fasta_ref '$fasta_ref'
---annot '$annot'
---snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
---summary '$text_outputs_dir/summary.txt'
---report '$text_outputs_dir/report.txt'
---calls '$text_outputs_dir/calls.txt'
---confidences '$text_outputs_dir/confidences.txt'
-if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
-    --sex '$text_outputs_dir/gender_estimate.txt'
-#end if
-#if str($append_version) == "no":
-    --no-version
-#end if
---output '$output'
---output_type $output_type
---threads \${GALAXY_SLOTS:-4}
-    ]]></command>
-    <inputs>
-        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
-        <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
-            <options from_data_table="all_fasta">
-                <column name="name" index="1"/>
-                <column name="value" index="2"/>
-                <column name="path" index="2"/>
-                <filter type="sort_by" column="1"/>
-                <validator type="no_options" message="No Fasta genome references are available.  Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/>
-            </options>
-        </param>
-        <conditional name="output_gender_estimate_cond">
-            <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes"/>
-        </conditional>
-        <conditional name="append_version_cond">
-            <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes"/>
-        </conditional>
-    </inputs>
-    <outputs>
-        <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
-            <discover_datasets pattern="__name__" directory="output" format="txt" />
-        </collection>
-        <data name="output" format="vcf" />
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-This tool converts Affymetrix genotype calls and intensity files to VCF format.
-
------
-
-**Required options**
-
-**Other options**
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{None,
-            journal = {None},
-            author = {Genovese, Giulio},
-            title = {None},
-            year = {None},
-            url = {https://github.com/freeseek/gtc2vcf},}
-        </citation>
-    </citations>
-</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Thu Oct 04 10:26:01 2018 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Oct 04 10:26:01 2018 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>