Mercurial > repos > galaxy-australia > ipa_hifi

comparison macros.xml @ 0:f78303e25f3e draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
author galaxy-australia
date Wed, 08 Feb 2023 04:31:08 +0000
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-1:000000000000 0:f78303e25f3e
1 <macros>
2 <token name="@TOOL_VERSION@">1.8.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="biotools">
5 <xrefs>
6 <xref type="bio.tools">ipa_hifi</xref>
7 </xrefs>
8 </xml>
9 <xml name="requirements">
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">pbipa</requirement>
12 </requirements>
13 </xml>
14 <xml name="stdio">
15 <stdio>
16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
17 <exit_code range="1:" level="fatal" description="Error" />
18 </stdio>
19 </xml>
20 <token name="@CONDA_IPA_PATH@">if [ -z "\$IPA_PATH" ]; then export IPA_PATH=\$(dirname \$(dirname \$(readlink -e \$(which ipa)))); fi</token>
21 <xml name="version_command">
22 <version_command><![CDATA[
23 if [ -z "$IPA_PATH" ]; then export IPA_PATH=$(dirname $(dirname $(readlink -e $(which ipa)))); fi &&
24 "$IPA_PATH/bin/ipa" --version 2>&1 | head -1
25 ]]></version_command>
26 </xml>
27 <xml name="macro_input">
28 <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file"/>
29 </xml>
30 <token name="@PREPARE_INPUT_FILE@">
31 <![CDATA[
32 #set $pacbio_input_file = 'input.fastq'
33 #if $input_file.is_of_type('fastq')
34 cp '$input_file' $pacbio_input_file
35 #elif $input_file.is_of_type('fasta')
36 #set $pacbio_input_file = 'input.fasta'
37 cp '$input_file' $pacbio_input_file
38 #elif $input_file.is_of_type('bam')
39 #set $pacbio_input_file = 'input.bam'
40 cp '$input_file' $pacbio_input_file
41 #end if
42 ]]>
43 </token>
44 <token name="@INPUT_FILE@">
45 $pacbio_input_file
46 </token>
47 <xml name="macro_inputs">
48 <param name="input_files" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file datasets" multiple="True" />
49 </xml>
50 <token name="@PREPARE_INPUT_FILES@">
51 <![CDATA[
52 #set $pacbio_input_files = []
53 #set $pacbio_list_file = 'pacbio_list'
54 #for (i, input_file) in enumerate($input_files):
55 #set $pacbio_input_file = 'input' + str($i) + '.fastq'
56 #if $pacbio_input_file.is_of_type('fastq')
57 cp '$input_file' $pacbio_input_file
58 #elif $input_file.is_of_type('fasta')
59 #set $pacbio_input_file = 'input' + str($i) + 'fasta'
60 cp '$input_file' $pacbio_input_file
61 #elif $input_file.is_of_type('bam')
62 #set $pacbio_input_file = 'input' + str($i) + 'bam'
63 cp '$input_file' $pacbio_input_file
64 #end if
65 echo '$pacbio_input_file' >> $pacbio_list_file &&
66 $pacbio_input_files.append($pacbio_input_file)
67 #end for
68 ]]>
69 </token>
70 <token name="@INPUT_FILES@">
71 #echo ' '.join($pacbio_input_files)#
72 </token>
73 <token name="@INPUT_LIST_FILE@">
74 $pacbio_list_file
75 </token>
76 </macros>