diff macros.xml @ 0:4069d17252b8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu May 18 09:35:35 2017 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0" ?>
+<macros>
+    <token name="@WRAPPER_VERSION@">1.9.1</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="citations">
+        <citation type="doi">10.1038/nmeth.f.303</citation>
+    </xml>
+
+    <xml name="pick_otus_reference_source">
+        <conditional name="references">
+            <param name="source_selector" type="select" label="Use reference sequences from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param argument="--refseqs_fp" label="Reference sequences" type="select">
+                    <options from_data_table="qiime_rep_set"/>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="pick_otus_similarity">
+        <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
+    </xml>
+    <xml name="pick_otus_denovo_otu_id_prefix">
+        <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
+    </xml>
+    <xml name="pick_otus_enable_rev_strand_match">
+        <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/>
+    </xml>
+    <xml name="pick_otus_suppress_presort_by_abundance_uclust">
+        <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/>
+    </xml>
+    <xml name="pick_otus_max">
+        <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
+        <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
+    </xml>
+    <xml name="pick_otus_stepwords">
+        <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
+    </xml>
+    <xml name="pick_otus_word_length">
+        <param argument="--word_length" type="integer" value="8" label="Word length value"/>
+    </xml>
+    <xml name="pick_otus_suppress_prefilter_exact_match">
+        <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
+    </xml>
+</macros>