diff macros.xml @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,96 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.7">python</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@URL@">
+https://cpt.tamu.edu/apollo
+  </token>
+  <token name="@AUTH@">
+@URL@
[e-mail]
+\$GALAXY_WEBAPOLLO_PASSWORD
+  </token>
+  <xml name="auth_file">
+    <param label="Apollo Authentication File"
+    name="apolloCredentialsFile" type="data" format="json" />
+  </xml>
+
+  <token name="@CN_OR_GUESS@">
+<![CDATA[
+#if $cn_source.source_select == "auto":
+    \$(cat $cn_source.cn_file | grep '^>' | head -n 1  | sed 's/\s.*//g;s/>//g')
+#elif $cn_source.source_select == "auto_json":
+    \$(cat $cn_source.cn_file | grep 'commonName' | head -n 1| sed 's/.*: "//g;s/".*//g')
+#else
+    "${cn_source.organism_cn}"
+#end if
+]]>
+  </token>
+  <xml name="cn_or_guess">
+    <conditional name="cn_source">
+        <param name="source_select" type="select" label="Organism Common Name Source">
+            <option value="auto">Autodetect from Fasta</option>
+            <option value="auto_json">Autodetect from Apollo JSON</option>
+            <option value="direct">Direct Entry</option>
+        </param>
+        <when value="auto">
+            <param name="cn_file" type="data" format="fasta" label="Organism Common Name" />
+        </when>
+        <when value="auto_json">
+            <param name="cn_file" type="data" format="json" label="Apollo Organism File" />
+        </when>
+        <when value="direct">
+            <param name="organism_cn" type="text" label="Organism Common Name" />
+        </when>
+    </conditional>
+  </xml>
+
+  <xml name="citations">
+      <citations>
+      </citations>
+  </xml>
+  <xml name="dummy">
+    <param label="Dummy Inputs" name="dummy" type="data" multiple="True" optional="True">
+        <help>
+            With workflows that contact remote databases, it is sometimes
+            necessary to have particular operations happen in a particular
+            order. I.e. you would not want to try and add data to an organism
+            if the organism did not yet exist in WebApollo.
+            Since few of the WebApollo2 toolsuite output files which are
+            used in a downstream task (e.g. the output adding an organism is
+            not used elsewhere), we provide this dummy option which lets you
+            select outputs to help provide context for when this task should
+            execute.
+        </help>
+    </param>
+  </xml>
+  <xml name="gff3_input">
+    <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
+  </xml>
+  <token name="@GENOME_SELECTOR_PRE@">
+#if $reference_genome.reference_genome_source == 'history':
+    ln -s $reference_genome.genome_fasta genomeref.fa;
+#end if
+  </token>
+  <token name="@GENOME_SELECTOR@">
+#if $reference_genome.reference_genome_source == 'cached':
+    "${reference_genome.fasta_indexes.fields.path}"
+#elif $reference_genome.reference_genome_source == 'history':
+    genomeref.fa
+#end if
+  </token>
+<token name="@REFERENCES@">
+<![CDATA[
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite:
+Eric Rasche (2016), `Galaxy wrapper <https://github.com/TAMU-CPT/galaxy-webapollo>`_
+]]>
+    </token>
+</macros>