Mercurial > repos > galaxy-australia > ipa_hifi

annotate macros.xml @ 1:1289beb50ab0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit a0de70c2d45cc307f303c82d30493c7d69e86604"
author galaxy-australia
date Mon, 13 Feb 2023 04:38:21 +0000
parents f78303e25f3e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
1 <macros>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.8.0</token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
4 <xml name="biotools">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
5 <xrefs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
6 <xref type="bio.tools">ipa_hifi</xref>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
7 </xrefs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
8 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
9 <xml name="requirements">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
10 <requirements>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">pbipa</requirement>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
12 </requirements>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
13 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
14 <xml name="stdio">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
15 <stdio>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
16 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
17 <exit_code range="1:" level="fatal" description="Error" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
18 </stdio>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
19 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
20 <token name="@CONDA_IPA_PATH@">if [ -z "\$IPA_PATH" ]; then export IPA_PATH=\$(dirname \$(dirname \$(readlink -e \$(which ipa)))); fi</token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
21 <xml name="version_command">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
22 <version_command><![CDATA[
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
23 if [ -z "$IPA_PATH" ]; then export IPA_PATH=$(dirname $(dirname $(readlink -e $(which ipa)))); fi &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
24 "$IPA_PATH/bin/ipa" --version 2>&1 | head -1
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
25 ]]></version_command>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
26 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
27 <xml name="macro_input">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
28 <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
29 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
30 <token name="@PREPARE_INPUT_FILE@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
31 <![CDATA[
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
32 #set $pacbio_input_file = 'input.fastq'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
33 #if $input_file.is_of_type('fastq')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
34 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
35 #elif $input_file.is_of_type('fasta')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
36 #set $pacbio_input_file = 'input.fasta'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
37 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
38 #elif $input_file.is_of_type('bam')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
39 #set $pacbio_input_file = 'input.bam'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
40 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
41 #end if
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
42 ]]>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
43 </token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
44 <token name="@INPUT_FILE@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
45 $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
46 </token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
47 <xml name="macro_inputs">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
48 <param name="input_files" type="data" format="fasta,fastq,fasta.gz,fastq.gz,bam,xml" label="Sequence file datasets" multiple="True" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
49 </xml>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
50 <token name="@PREPARE_INPUT_FILES@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
51 <![CDATA[
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
52 #set $pacbio_input_files = []
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
53 #set $pacbio_list_file = 'pacbio_list'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
54 #for (i, input_file) in enumerate($input_files):
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
55 #set $pacbio_input_file = 'input' + str($i) + '.fastq'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
56 #if $pacbio_input_file.is_of_type('fastq')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
57 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
58 #elif $input_file.is_of_type('fasta')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
59 #set $pacbio_input_file = 'input' + str($i) + 'fasta'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
60 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
61 #elif $input_file.is_of_type('bam')
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
62 #set $pacbio_input_file = 'input' + str($i) + 'bam'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
63 cp '$input_file' $pacbio_input_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
64 #end if
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
65 echo '$pacbio_input_file' >> $pacbio_list_file &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
66 $pacbio_input_files.append($pacbio_input_file)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
67 #end for
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
68 ]]>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
69 </token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
70 <token name="@INPUT_FILES@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
71 #echo ' '.join($pacbio_input_files)#
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
72 </token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
73 <token name="@INPUT_LIST_FILE@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
74 $pacbio_list_file
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
75 </token>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
76 </macros>