diff kobas_macros.xml @ 0:720b1beabad6 draft

planemo upload commit 5dd86ae785ae71f697aab8ede735f394b39ad7bc-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kobas_macros.xml	Sat Nov 05 09:20:51 2016 -0400
@@ -0,0 +1,60 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">0.3</token>
+    <token name="@KOBAS_VERSION@">2.1.1</token>
+    <xml name="input_kobasdb">
+        <param
+            name="species"
+            type="text"
+            label="Species abbreviation"
+            argument="--species"
+            help="For example: ko for KEGG
+                        Orthology, hsa for Homo sapiens, mmu for Mus musculus,
+                        dme for Drosophila melanogaster, ath for Arabidopsis
+                        thaliana, sce for Saccharomyces cerevisiae and eco for
+                        Escherichia coli K-12 MG1655"/>
+        <param format="sqlite" name="kobasdb" type="data" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
+    </xml>
+    <xml name="blastdb_selector">
+        <param name="choice" type="select" label="BLAST Protein database">
+            <option value="histdb">BLAST database from your history</option>
+            <option value="fasta">BLAST database from FASTA File</option>
+            <option value="local" selected="True">Locally installed BLAST database</option>
+        </param>
+        <when value="fasta">
+            <param name="fastadb" format="fasta" type="data" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/>
+            <param name="histdb" type="hidden" value=""/>
+            <param name="fasta" type="hidden" value=""/>
+        </when>
+        <when value="histdb">
+            <param name="localdb" type="hidden" value=""/>
+            <param name="fastadb" type="hidden" value=""/>
+            <param
+                name="histdb"
+                type="data"
+                format="blastdbp"
+                label="Protein BLAST database"
+                help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
+        </when>
+        <when value="local">
+            <param name="localdb" type="select" label="Protein BLAST database">
+                <options from_data_table="blastdb_p"/>
+            </param>
+            <param name="histdb" type="hidden" value=""/>
+            <param name="fastadb" type="hidden" value=""/>
+        </when>
+    </xml>
+    <xml name="kobas_citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gkr483</citation>
+        </citations>
+    </xml>
+
+    <token name="@HELP_KOBAS_INFO@">
+**KOBAS**
+
+KOBAS is a KEGG Orthology Based Annotation System. Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. The necessary KOBAS databases for multiple species can be downloaded from http://kobas.cbi.pku.edu.cn/download.php
+    </token>
+    <token name="@HELP_KOBAS_URL@">
+        KOBAS can be accessed at http://kobas.cbi.pku.edu.cn
+    </token>
+</macros>