changeset 8:35f9b833e12b draft default tip

planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9

--- a/usearch-wrapper.sh	Mon Oct 12 15:59:59 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-RDP_SEQS="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.fasta"
-RDP_SEQINFO="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.seq_info.csv"
-
-sqlite3 -csv -header ${CLASS_DB} <<EOF > usearch_meta.csv
-SELECT pn.name, CAST(pn.mass AS INT) count, tax_id, tax_name, taxa.rank
-  FROM multiclass_concat
-    JOIN taxa USING (tax_id)
-    JOIN placement_names pn USING (placement_id, name)
-    WHERE want_rank = 'species';
-EOF
-
-romp -v usearch_clusters \
-    --usearch-quietly \
-    --query-group tax_id \
-    --query-duplication count \
-    --database-name seqname \
-    --database-group tax_id \
-    ${INPUT_SEQS} \
-    usearch_meta.csv \
-    ${RDP_SEQS} \
-    ${RDP_SEQINFO} \
-    ${USEARCH_HITS} \
-    ${USEARCH_GROUPS}

--- a/usearch.xml	Mon Oct 12 15:59:59 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="PHYLO_usearch" name="Analyze sequences" version="1.1.0">
-  <description>with USEARCH</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <version_command>/home/matsengrp/local/bin/usearch6_64 --version</version_command>
-  <command interpreter="bash">
-    usearch-wrapper.sh $config
-  </command>
-  <inputs>
-    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
-    <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
-  </inputs>
-  <outputs>
-    <data format="csv" name="usearch_hits" label="USEARCH hits"/>
-    <data format="csv" name="usearch_groups" label="USEARCH groups"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-INPUT_SEQS="${input_seqs}"
-CLASS_DB="${class_db}"
-
-USEARCH_HITS="${usearch_hits}"
-USEARCH_GROUPS="${usearch_groups}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool queries large sequence databases for target sequences and assigns
-those sequences to clusters.
-
-  </help>
-  <citations>
-    <expand macro="cite_usearch"/>
-  </citations>
-</tool>