--- a/gemini_macros.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.10.0">gemini</requirement>
-            <requirement type="package" version="0.1.3">grabix</requirement>
-            <requirement type="package" version="0.2.6">tabix</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
-            <requirement type="package" version="2.19.1">bedtools</requirement>
-            <yield />
-        </requirements>
-    </xml>
-
-    <xml name="version_command">
-        <version_command>gemini --version</version_command>
-    </xml>
-
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" />
-            <exit_code range=":-1" />
-            <regex match="Error:" />
-            <regex match="Exception:" />
-        </stdio>
-    </xml>
-
-    <xml name="annotation_dir">
-        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
-            <options from_data_table="gemini_databases">
-                <filter type="sort_by" column="0" />
-                <validator type="no_options" message="No annotation database is available" />
-            </options>
-        </param>
-    </xml>
-
-    <xml name="add_header_column">
-        <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" 
-            label="Add a header of column names to the output" help="(--header)"/>
-    </xml>
-
-    <xml name="radius">
-        <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
-            <validator type="in_range" min="0"/>
-        </param>
-    </xml>
-    <xml name="variant_mode">
-        <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" 
-            label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
-    </xml>
-
-    <xml name="column_filter">
-        <conditional name="report">
-            <param name="report_selector" type="select" label="Columns to include in the report"
-                help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
-                <option value="all" selected="True">all</option>
-                <option value="column_filter">User given columns</option>
-            </param>
-            <when value="all"/>
-            <when value="column_filter">
-                <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
-                    <option value="gene">gene</option>
-                    <option value="chrom">chrom</option>
-                    <option value="start">start</option>
-                    <option value="end">end</option>
-                    <option value="ref">ref</option>
-                    <option value="alt">alt</option>
-                    <option value="impact">impact</option>
-                    <option value="impact_severity">impact_severity</option>
-                </param>
-            </when>
-        </conditional>
-    </xml>
-
-    <xml name="filter">
-        <conditional name="filter">
-            <param name="filter_selector" type="select" label="Apply additional constraints"
-                help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.">
-                <option value="no">No additional constraints</option>
-                <option value="yes">Apply additional constraints</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param name="filter" type="text" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)">
-                    <expand macro="sanitize_query" />
-                </param>
-            </when>
-        </conditional>
-    </xml>
-
-    <xml name="sanitize_query">
-        <sanitizer invalid_char="">
-            <valid initial="string.printable"/>
-       </sanitizer>
-    </xml>
-
-    <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
-        #if str($filter.filter_selector) == 'yes' and $filter.filter:
-            #import pipes
-            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
-        #end if
-    </token>
-
-    <xml name="min_sequence_depth">
-        <param name="d" type="integer" value="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
-                help="default: 0 (-d)">
-            <validator type="in_range" min="0"/>
-        </param>
-    </xml>
-
-    <token name="@VERSION@">0.10.1</token>
-
-    <token name="@CITATION@">------
-
-**Citation**
-
-If you use GEMINI in your research, please cite the following manuscript:
-
-  </token>
-  <xml name="citations">
-    <citations>
-        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
-        <yield />
-    </citations>
-  </xml>
-
-    <xml name="infile">
-        <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
-            <options options_filter_attribute="metadata.gemini_version" >
-                <filter type="add_value" value="@VERSION@" />
-            </options>
-            <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>
-        </param>
-    </xml>
-
-</macros>