Mercurial > repos > iuc > medaka_variant_pipeline

comparison macros.xml @ 9:336b3def9b2b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 2a29f6676b1bbf42e9c4c3edeb4471a0ac57fbe3"
author iuc
date Mon, 29 Mar 2021 20:06:01 +0000
parents 5c959a2dde5f
children 7623e5888be9
comparison
equal deleted inserted replaced
8:1040a307be0c 9:336b3def9b2b
27 command 27 command
28 --> 28 -->
29 29
30 <token name="@REF_FASTA@"><![CDATA[ 30 <token name="@REF_FASTA@"><![CDATA[
31 #if $reference_source.reference_source_selector == 'history': 31 #if $reference_source.reference_source_selector == 'history':
32 ln -f -s '$reference_source.ref_file' reference.fa && 32 #if $reference_source.ref_file.ext.endswith(".gz")
33 gunzip -c '$reference_source.ref_file' > reference.fa &&
34 #else
35 ln -f -s '$reference_source.ref_file' reference.fa &&
36 #end if
33 #else: 37 #else:
34 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 38 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
35 #end if 39 #end if
36 ]]></token> 40 ]]></token>
37 41
83 </options> 87 </options>
84 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 88 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
85 </param> 89 </param>
86 </when> 90 </when>
87 <when value="history"> 91 <when value="history">
88 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> 92 <param name="ref_file" type="data" format="fasta,fasta.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
89 </when> 93 </when>
90 </conditional> 94 </conditional>
91 </xml> 95 </xml>
92 96
93 <!-- 97 <!--