# HG changeset patch
# User greg
# Date 1696944195 0
# Node ID fb6a4e2d623409fbe0751db38be5e7aedf97c670

Uploaded

diff -r 000000000000 -r fb6a4e2d6234 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Oct 10 13:23:15 2023 +0000
@@ -0,0 +1,9 @@
+name: pyfaidx
+owner: greg
+description: Runs faidx to index the input FASTA file.
+long_description: Runs faidx to index the input FASTA file.
+categories: 
+- Next Gen Mappers
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/mapping/pyfaidx
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r fb6a4e2d6234 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 10 13:23:15 2023 +0000
@@ -0,0 +1,16 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.7.2.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">pyfaidx</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7287/peerj.preprints.970v1</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r fb6a4e2d6234 pyfaidx.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyfaidx.xml	Tue Oct 10 13:23:15 2023 +0000
@@ -0,0 +1,40 @@
+<tool id="pyfaidx" name="pyfaidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description>efficient FASTA indexing</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#if $input.is_of_type('fasta.gz'):
+    gunzip -c '$input' > 'input.fasta' &&
+#else:
+    ln -s '$input' 'input.fasta' &&
+#end if
+faidx -i chromsizes 'input.fasta' > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.fasta.gz" ftype="fasta.gz"/>
+            <output name="output" ftype="fasta">
+                <assert_contents>
+                    <has_size value="51690"/>
+                    <has_text text=">contig_10"/>
+                    <has_text text=">contig_7"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Runs faidx to index the input FASTA file.   
+    </help>
+    <expand macro="citations"/>
+</tool>
+
diff -r 000000000000 -r fb6a4e2d6234 test-data/input.fasta.gz
Binary file test-data/input.fasta.gz has changed