# HG changeset patch
# User greg
# Date 1677011797 0
# Node ID 46d31ec5d24c5906e1d1a525c70fdc1bccef2231
# Parent  33a0ea992043dcc7fc4dfa608439e8de1c55ecad
Uploaded

diff -r 33a0ea992043 -r 46d31ec5d24c .shed.yml
--- a/.shed.yml	Tue Feb 21 19:55:42 2023 +0000
+++ b/.shed.yml	Tue Feb 21 20:36:37 2023 +0000
@@ -1,7 +1,7 @@
 name: draw_amr_matrix
 owner: greg
-description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix.
-long_description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix.
+description: Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene drug mappings file and draws an AMR matrix.
+long_description: Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene drug mappings file and draws an AMR matrix.
 categories: 
 - Visualization
 remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/draw_amr_matrix
diff -r 33a0ea992043 -r 46d31ec5d24c all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Tue Feb 21 20:36:37 2023 +0000
@@ -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.
+#
diff -r 33a0ea992043 -r 46d31ec5d24c test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Tue Feb 21 20:36:37 2023 +0000
@@ -0,0 +1,1 @@
+ref_genome	ref_genome	ref_genome	${__HERE__}/ref_genome.fasta
diff -r 33a0ea992043 -r 46d31ec5d24c tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Feb 21 20:36:37 2023 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 33a0ea992043 -r 46d31ec5d24c tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Feb 21 20:36:37 2023 +0000
@@ -0,0 +1,8 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>
+