# HG changeset patch
# User yhoogstrate
# Date 1438692835 14400
# Node ID 39d95e2675f59447b2a55ff50b9d31ff3a0f44dc
# Parent  131c32c22de90d5a3150352996b76c0713c35744
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a

diff -r 131c32c22de9 -r 39d95e2675f5 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Aug 04 08:53:55 2015 -0400
@@ -0,0 +1,7 @@
+CrossMap wrapper for Galaxy
+===========================
+
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
diff -r 131c32c22de9 -r 39d95e2675f5 crossmap.xml
--- a/crossmap.xml	Wed Jul 22 08:31:24 2015 -0400
+++ b/crossmap.xml	Tue Aug 04 08:53:55 2015 -0400
@@ -1,49 +1,238 @@
-<tool id="crossmap" name="crossmap" version="0.1.8">
+<tool id="crossmap" name="CrossMap" version="0.1.9">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     
     <requirements>
-        <requirement type="package" version="0.1.8">crossmap</requirement>
+        <requirement type="package" version="0.1.9">crossmap</requirement>
     </requirements>
     
     <stdio></stdio>
 
     <command>
-        CrossMap.py --help > $output
+        CrossMap.py
+            $multiple.input_format
+            
+            #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
+                <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
+                "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
+            #else
+                "$multiple.seq_source.input_chain"
+            #end if
+            
+            #if $multiple.input_format == "bam"
+                -m $multiple.insert_size
+                -s $multiple.insert_size_stdev
+                -t $multiple.insert_size_fold
+            #end if
+            
+            "$multiple.seq_source.input"
+            
+            #if $multiple.input_format == "vcf"
+                "$multiple.seq_source.input_fasta"
+            #end if 
+            
+            $output
     </command>
 
     <inputs>
-        <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of" />
-        <!--
-        <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of">
-            <validator type="unspecified_build" />
-            <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
-        </param>
-        <param name="to_dbkey" type="select" label="To">
-            <options from_file="liftOver.loc">
-                <column name="name" index="1"/>
-                <column name="value" index="2"/>
-                <column name="dbkey" index="0"/>
-                <filter type="data_meta" ref="input" key="dbkey" column="0" />
-            </options>
-        </param>
-        <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
         <conditional name="multiple">
-                <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
-                        <option value="0" selected="true">No</option>
-                        <option value="1">Yes</option>
-                </param>
-                <when value="0">
-                        <param name="minSizeQ" type="hidden" value="0" />
-                        <param name="minChainQ" type="hidden" value="0" />
-                        <param name="minChainT" type="hidden" value="0" />
-                </when>
-                <when value="1">
-                        <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/>
-                        <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/>
-                        <param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
-                </when>
+            <param name="input_format" type="select" label="Convert a file of the following format">
+                <option value="bam">BAM or SAM format</option>
+                <option value="bed">BED or BED-like</option>
+                <option value="bigwig">BigWig</option>
+                <option value="gff">GFF or GTF</option>
+                <option value="vcf">VCF</option>
+                <option value="wig">Wiggle or bedGraph</option>
+            </param>
+            <when value="bam">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history">From History</option>
+                    </param>
+                        <when value="cached">
+                            <param type="data" format="bam,sam" name="input" label="BAM/SAM file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            <param name="input_chain" type="select" label="Lift Over To">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1"/>
+                                    <column name="value" index="2"/>
+                                    <column name="dbkey" index="0"/>
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
+                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                        </when>
+                </conditional>
+                
+                <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
+                <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
+                <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
+            </when>
+            <when value="bed">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history">From History</option>
+                    </param>
+                        <when value="cached">
+                            <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            <param name="input_chain" type="select" label="Lift Over To">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1"/>
+                                    <column name="value" index="2"/>
+                                    <column name="dbkey" index="0"/>
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
+                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                        </when>
+                </conditional>
+            </when>
+            <when value="bigwig">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history">From History</option>
+                    </param>
+                        <when value="cached">
+                            <param format="bigwig" name="input" type="data" label="BigWig file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            <param name="input_chain" type="select" label="Lift Over To">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1"/>
+                                    <column name="value" index="2"/>
+                                    <column name="dbkey" index="0"/>
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param format="bigwig" name="input" type="data" label="BigWig file" />
+                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                        </when>
+                </conditional>
+            </when>
+            <when value="gff">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history">From History</option>
+                    </param>
+                        <when value="cached">
+                            <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            <param name="input_chain" type="select" label="Lift Over To">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1"/>
+                                    <column name="value" index="2"/>
+                                    <column name="dbkey" index="0"/>
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" />
+                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                        </when>
+                </conditional>
+            </when>
+            <when value="vcf">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history_chain">Chain file from History</option>
+                        <option value="history_all">Chain &amp; FASTA files from History</option>
+                    </param>
+                        <when value="cached">
+                            <param type="data" format="vcf" name="input" label="VCF file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            
+                            <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
+                            <param name="input_chain" type="select" label="Lift Over To (Chain file)">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1" />
+                                    <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter -->
+                                    <column name="dbkey" index="0" />
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                            
+                            <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
+                                <options from_file="all_fasta.loc">
+                                    <column name="name" index="2"/>
+                                    <column name="value" index="3"/>
+                                    <column name="dbkey" index="1"/>
+                                    <filter type="param_value" ref="input_chain" column="1" />
+                                </options>
+                            </param>
+                        </when>
+                        
+                        <when value="history_chain">
+                            <param type="data" format="vcf" name="input" label="VCF file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
+                            </param>
+                            <param type="data"  name="input_chain" multiple="false" label="LiftOver chain file" />
+                            <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
+                                <options from_file="all_fasta.loc">
+                                    <column name="name" index="2"/>
+                                    <column name="value" index="3"/>
+                                    <column name="dbkey" index="1"/>
+                                </options>
+                            </param>
+                        </when>
+                        
+                        <when value="history_all">
+                            <param type="data" format="vcf"   name="input" label="VCF file" />
+                            <param type="data"                name="input_all_chain" multiple="false" label="LiftOver chain file" />
+                            <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" />
+                        </when>
+                </conditional>
+            </when>
+            <when value="wig">
+                <conditional name="seq_source">
+                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
+                        <option value="cached">Local data (in galaxy)</option>
+                        <option value="history">From History</option>
+                    </param>
+                        <when value="cached">
+                            <param format="wig" name="input" type="data" label="Wiggle file">
+                                <validator type="unspecified_build" />
+                                <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
+                            </param>
+                            <param name="input_chain" type="select" label="Lift Over To">
+                                <options from_file="liftOver.loc">
+                                    <column name="name" index="1"/>
+                                    <column name="value" index="2"/>
+                                    <column name="dbkey" index="0"/>
+                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
+                                </options>
+                            </param>
+                        </when>
+                        <when value="history">
+                            <param format="wig" name="input" type="data" label="Wiggle file" />
+                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                        </when>
+                </conditional>
+            </when>
         </conditional>
-        -->
     </inputs>
     
     <outputs>
@@ -59,7 +248,7 @@
     </tests>
     
     <help>
-        CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
 and VCF, reading from remote servers and file compression are supported.
diff -r 131c32c22de9 -r 39d95e2675f5 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 22 08:31:24 2015 -0400
+++ b/tool_dependencies.xml	Tue Aug 04 08:53:55 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="crossmap" version="0.1.8">
-        <repository changeset_revision="ebe9034b7450" name="package_crossmap_0_1_8" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="crossmap" version="0.1.9">
+        <repository changeset_revision="57ecb6f23ec3" name="package_crossmap_0_1_9" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>