Mercurial > repos > iuc > crossmap_vcf

changeset 2:7a3c34157901 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
author iuc
date Fri, 20 Oct 2017 11:34:06 -0400
parents a40d9af7d058
children 9db73ff23c9f
files crossmap_vcf.xml macros.xml test-data/cached_locally/liftOver.loc
diffstat 3 files changed, 7 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_vcf.xml	Fri Oct 20 02:51:15 2017 -0400
+++ b/crossmap_vcf.xml	Fri Oct 20 11:34:06 2017 -0400
@@ -14,9 +14,9 @@
 
 #if $seq_source.index_source_s == "cached"
     ## This is the 2nd dbkey, and the corresponding value has to be looked up
-    "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
+    "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
 #else
-    '${chain_source.input_chain}'
+    '${seq_source.chain_source.input_chain}'
 #end if
 
 '${input_file}'
@@ -45,14 +45,17 @@
                 <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_data_table="all_fasta"/>
                 </param>
+
+                <expand macro="chain" />
             </when>
 
             <when value="history">
                 <param name="input" type="data" format="vcf" label="VCF file"/>
                 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
+
+                <expand macro="chain" />
             </when>
         </conditional>
-        <expand macro="chain" />
     </inputs>
 
     <outputs>
--- a/macros.xml	Fri Oct 20 02:51:15 2017 -0400
+++ b/macros.xml	Fri Oct 20 11:34:06 2017 -0400
@@ -28,9 +28,7 @@
             <when value="cached">
                 <param name="input_chain" type="select" label="Lift Over To">
                     <options from_data_table="liftOver">
-                        <!--
                         <filter type="data_meta" ref="input" key="dbkey" column="0"/>
-                        -->
                     </options>
                 </param>
             </when>
--- a/test-data/cached_locally/liftOver.loc	Fri Oct 20 02:51:15 2017 -0400
+++ b/test-data/cached_locally/liftOver.loc	Fri Oct 20 11:34:06 2017 -0400
@@ -29,4 +29,4 @@
 #anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
 #...etc...
 
-A	B	${__HERE__}/aToB.over.chain
+hg18	hg19	${__HERE__}/aToB.over.chain