diff lastz_macros.xml @ 5:bd84ff27bc16 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lastz_macros.xml	Mon Feb 26 15:37:53 2018 -0500
@@ -0,0 +1,41 @@
+<macros>
+    <token name="@LASTZ_CONDA_VERSION@">1.0.4</token>
+    <token name="@TARGET_INPUT_COMMAND_LINE@">
+        #if $source.ref_source=="history":
+            '${source.target}'
+        #else:
+            '${source.target_2bit.fields.path}'
+        #end if
+    </token>
+    <xml name="target_input">
+        <conditional name="source">
+            <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option">
+                <option value="cached">locally cached</option>
+                <option value="history">from your history</option>
+            </param>
+            <when value="cached">
+                <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="lastz_seqs" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+            @misc{
+                githublastz,
+                author = {Harris, Robert},
+                year = {2007},
+                title = {Improved pairwise alignment of genomic DNA},
+                publisher = {The Pennsylvania State University},
+                journal = {Ph. D. Thesis},
+                url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf},
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>