annotate ipa.xml @ 0:f78303e25f3e draft

"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
parents
children 1289beb50ab0
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 <tool id="ipa" name="Improved Phased Assembler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
2 <description>IPA HiFi Genome Assembler</description>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
3 <macros>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
4 <import>macros.xml</import>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
5 </macros>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
6 <expand macro="requirements" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
7 <expand macro="stdio" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
8 <expand macro="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
9 <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
10 @CONDA_IPA_PATH@ &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
11 @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
12
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
13 ipa local
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
14 #if $ipa_params.no_polish:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
15 --no-polish
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
16 #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
17 #if $ipa_params.no_phase:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
18 --no-phase
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
19 #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
20 #if $ipa_params.no_purge_dups:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
21 --no-purge-dups
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
22 #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
23 #if $ipa_params.genome_size:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
24 --genome-size '$ipa_params.genome_size'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
25 #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
26 #if $ipa_params.coverage:
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
27 --coverage '$ipa_params.coverage'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
28 #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
29 --nthreads \${GALAXY_SLOTS:-2} --njobs \${GALAXY_SLOTS:-4} -i $pacbio_input_file --only-print &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
30
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
31 sed -i '/^reads_fn:.*$/d' 'RUN/config.yaml' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
32
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 $ipa_advance_params.advance_options.adv_opt == 'True':
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
34 sed -i '/^advanced_options:.*$/d' 'RUN/config.yaml' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
35 cat $add_advance_options >> 'RUN/config.yaml' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
36 #end if
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
37 cat 'RUN/ipa.log' > '$log' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
38 cat 'RUN/input.fofn' > '$fofn' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
39 cat 'RUN/config.yaml' > '$config' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
40 cat $fofn | awk '{print "\nreads_fn: " $1}' >> '$config' &&
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
41 python3 -m snakemake -j \${GALAXY_SLOTS:-6} -p -s "\$IPA_PATH/etc/ipa.snakefile" --configfile '$config' --reason
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
42 ]]></command>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
43 <configfiles>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
44 <configfile name="add_advance_options"><![CDATA[
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
45 #if str($ipa_advance_params.advance_options.adv_opt) == 'True':
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
46 advanced_options: 'config_auto_comp_max_cov=$ipa_advance_params.advance_options.auto_comp_max_cov;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
47 config_block_size=$ipa_advance_params.advance_options.block_size;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
48 config_ovl_filter_opt=$ipa_advance_params.advance_options.ovl_filter_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
49 config_ovl_min_idt=$ipa_advance_params.advance_options.ovl_min_idt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
50 config_ovl_min_len=$ipa_advance_params.advance_options.ovl_min_len;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
51 config_ovl_opt=$ipa_advance_params.advance_options.ovl_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
52 config_phasing_opt=$ipa_advance_params.advance_options.phasing_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
53 config_phasing_split_opt=$ipa_advance_params.advance_options.phasing_split_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
54 config_seeddb_opt=$ipa_advance_params.advance_options.seeddb_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
55 config_seqdb_opt=$ipa_advance_params.advance_options.seqdb_opt;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
56 config_use_hpc=$ipa_advance_params.advance_options.use_hpc;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
57 config_use_seq_ids=$ipa_advance_params.advance_options.use_seq_ids;'
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
58 #end if]]></configfile>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
59 </configfiles>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
60 <inputs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
61 <expand macro="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
62 <section name="ipa_params" title="common options" expanded="false">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
63 <param name="no_polish" argument="polish" type="boolean" truevalue="--no-polish" falsevalue="" checked="False" label="Skip polishing. (default: no)" help="Polishing will be applied if the setting of this parameter is disable. (polish)" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
64 <param name="no_phase" argument="phase" type="boolean" truevalue="--no-phase" falsevalue="" checked="False" label="Skip phasing. (default: no)" help="Phasing will be applied if the setting of this parameter is disable. (phase)" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
65 <param name="no_purge_dups" argument="purge-dups" type="boolean" truevalue="--no-purge-dups" falsevalue="" checked="False" label="Skip purge_dups. (default: no)" help="Purge duplicates will be applied if the setting of this parameter is disable. (purge-dups)" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
66 <param name="genome_size" argument="--genome-size" type="integer" value="0" label="Genome Size, required only for downsampling. (default: 0)"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
67 <param name="coverage" argument="--coverage" type="integer" value="0" label="Downsmapled coverage, only if genome_size * coverage > 0. (default: 0)"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
68 </section>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
69 <section name="ipa_advance_params" title="advance options" expanded="false">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
70 <conditional name="advance_options">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
71 <param name="adv_opt" type="select" label="Specify advance options">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
72 <option value="True">Enabled</option>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
73 <option value="False" selected="True">Disabled</option>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
74 </param>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
75 <when value="True">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
76 <param name="auto_comp_max_cov" type="integer" value="1" help="These options are used to determine potential repoeats and filter out those reads before the string graph is constructed. 0 disables this feature; 1 enables it."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
77 <param name="block_size" type="integer" value="4096" help="The overlapping process is performed on pairs of blocks of input sequences, where each block contains the number of sequences which crop up to this size (in Mbp)"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
78 <param name="ovl_filter_opt" type="text" value="--max-diff 80 --max-cov 100 --min-cov 2 --bestn 10 --min-len 4000 --gapFilt --minDepth 4 --idt-stage2 98" help="see options"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
79 <param name="ovl_min_idt" type="integer" value="98" help="The final overlap identity threshold. Applied during the final filtering stage, right before the overlaps are passed to the layout stage."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
80 <param name="ovl_min_len" type="integer" value="1000" help="The minimum length of either A-read or a B-read to keep the overlap. Applied during the final filtering stage, right before the overlaps are passed to the layout stage."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
81 <param name="ovl_opt" type="text" value="--one-hit-per-target --min-idt 96" help="The defaults used here are: --one-hit-per-target which keeps only the best hit in case there are multiple possible overlaps between a pair of reads (tandem repeats); and --min-idt 96 which will filter out any overlap with identity lower than 96%"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
82 <param name="phasing_opt" type="text" value="" help="Options for the phasing tool nighthawk. The options set by this parameter are passed directly to nighthawk. For details on nighthawk options"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
83 <param name="phasing_split_opt" type="text" value="--split-type noverlaps --limit 3000000" help="Options that control the chunking of the phasing jobs, and through that regulate the time and memory consumption of each individual chunk. The defaults are: --split-type noverlaps which splits the chunks by the number of overlaps; and --limit 3000000 which allow at most approximately 3 million overlaps per chunk."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
84 <param name="seeddb_opt" type="text" value="-k 30 -w 80 --space 1" help="Options to control the seed computation.These options are passed directly to the pancake seeddb command. Defaults: -k 30 is the k-mer size of 30bp; -w 80 is the minimizer window size of 80bp; and --space 1 specifies the spacing for spaced seed construction, with 1 gap in between every two bases of the seed."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
85 <param name="seqdb_opt" type="text" value="--compression 1" help="Options to control the construction of the sequence database. These options are passed directly to the pancake seqdb command.Current default is --compression 1 which turns on the 2-bit encoding compression of the sequences."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
86 <param name="use_hpc" type="integer" value="0" help="This parameter enables (1) or disables (0) an experimental Homopolymer Compression feature."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
87 <param name="use_seq_ids" type="integer" value="1" help="This feature is mostly useful for debugging purposes. If 0 is specified, then the overlaps contain original sequence names instead of their numerical IDs."/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
88 </when>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
89 <when value="False">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
90 </when>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
91 </conditional>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
92 </section>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
93 </inputs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
94 <outputs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
95 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
96 <data name="fofn" format="txt" label="${tool.name} on ${on_string}: fofn" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
97 <data name="config" format="txt" label="${tool.name} on ${on_string}: config" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
98
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
99
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
100 <data format="fasta" name="purged_primary" label="final_purged_primary.fasta" from_work_dir="18-purge_dups/final_purged_primary.fasta" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
101 <data format="fasta" name="purged_haplotig" label="final_purged_haplotigs.fasta" from_work_dir="18-purge_dups/final_purged_haplotigs.fasta" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
102 <data format="fasta" name="primary_contig" label="primary_final.p_ctg.fasta" from_work_dir="19-final/final.p_ctg.fasta" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
103 <data format="fasta" name="alternative_contig" label="alternative_final.a_ctg.fasta" from_work_dir="19-final/final.a_ctg.fasta" />
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
104 </outputs>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
105
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
106 <tests>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
107 <test>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
108 <!-- #1 test with common parameters -->
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
109 <param name="input_file" value="test.bam"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
110 <section name="ipa_params">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
111 <param name="no_polish" argument="--no-polish" type="boolean" truevalue="--no-polish" falsevalue="" checked="True"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
112 <param name="no_phase" argument="--no-phase" type="boolean" truevalue="--no-phase" falsevalue="" checked="True"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
113 <param name="no_purge_dups" argument="--no-purge-dups" type="boolean" truevalue="--no-purge-dups" falsevalue="" checked="True"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
114 <param name="genome_size" argument="--genome-size" type="integer" value="0"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
115 <param name="coverage" argument="--coverage" type="integer" value="0"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
116 </section>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
117 <output name="log" value="log.txt" format="txt">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
118 <assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
119 <has_n_lines n="31"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
120 <has_size value="1470"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
121 </assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
122 </output>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
123 <output name="purged_primary" value="final_purged_primary.fasta" format="fasta">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
124 <assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
125 <has_size value="80515"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
126 </assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
127 </output>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
128 <output name="purged_haplotig" value="final_purged_haplotigs.fasta" format="fasta">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
129 <assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
130 <has_size value="0"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
131 </assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
132 </output>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
133 <output name="primary_contig" value="primary_ctg.fasta" format="fasta">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
134 <assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
135 <has_size value="80515"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
136 </assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
137 </output>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
138 <output name="alternative_contig" value="alternative_ctg.fasta" format="fasta">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
139 <assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
140 <has_size value="0"/>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
141 </assert_contents>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
142 </output>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
143 </test>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
144 </tests>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
145 <help><![CDATA[
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
146 .. class:: infomark
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
147
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
148 **What it does**
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
149
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
150 *Improved Phased Assembly (IPA)* is a HIFI Genome Assembler
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
151
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
152 **Input**
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
153
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
154 - input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
155
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
156
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
157 **Output**
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
158
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
159 *Assembly*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
160
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
161 - primary_final : file containing assembled primary purged duplicated contigs (FASTA format)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
162 - alternative_final : file containing assembled alternative purged duplicated contigs (FASTA format)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
163 - final_purged_primary : file containing assembled primary contigs (FASTA format)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
164 - final_purged_haplotigs : file containing assembled haplotigs (FASTA format)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
165
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
166 *Config file*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
167
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
168 The description of the config file.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
169
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
170 *Common Parameter*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
171
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
172 - reads_fn: Can be a FOFN, FASTA, FASTQ, BAM or XML. Also, gzipped versions of FASTA and FASTQ are available. This IPA wrapper has excluded the FOFN and XML from the input option.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
173 - genome_size: Used for downsampling in combination with coverage. If genome_size * coverage <=0 downsampling is turned off.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
174 - coverage: Used for downsampling in combination with genome_size. If genome_size * coverage <=0 downsampling is turned off.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
175 - advanced_options: A single line listing advanced options in the form of key = value pairs, separated with ;.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
176 - polish_run: Polishing will be applied if the value of this parameter is equal to 1.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
177 - phase_run: Phasing will be applied if the value of this parameter is equal to 1.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
178 - nproc: Number of threads to use on each compute node.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
179 - max_nchunks: Parallel tasks will be groupped into at most this many chunks. If there is more than one task per chunk, they are executed linearly. Each chunk is executed in parallel. Useful for throttling job submissions.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
180 - tmp_dir: Temporary directory which will be used for some disk-based operations, like sorting.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
181
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
182 *Advance Parameter*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
183
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
184 - config_autocomp_max_cov=1 : If enabled, the maximum allowed overlap coverage at either the 5’ or the 3’ end of every read is automatically determined based on the statistics computed from the overlap piles. s. This value is appended to the config_ovl_filter_opt value internally, and supersedes the manually specified --max-cov and --max-diff values of that parameter. These options are used to determine potential repeats and filter out those reads before the string graph is constructed. 0 disables this feature; 1 enables it.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
185 - config_block_size=4096 : The overlapping process is performed on pairs of blocks of input sequences, where each block contains the number of sequences which crop up to this size (in Mbp). Note: The number of pairwise comparisons grows quadratically with the number of blocks (meaning more cluster jobs), but also the larger the block size the more resources are required to execute each pairwise comparison.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
186 - config_coverage=0 : The input Data Set can be downsampled to a desired coverage, provided that both the Downsampled coverage and Genome Length parameters are specified and above 0. Downsampling applies to the entire assembly process, including polishing. This feature selects reads randomly, using a fixed random seed for reproducibility.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
187 - config_existing_db_prefix= : Allows injection of an existing SeqDB, so that one doesn’t have to be built from scratch. The provided existing DB is symbolically linked and used for assembly. (This option is intended for debugging purposes.)
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
188 - config_genome_size=0 : The approximate number of base pairs expected in the genome, used to determine the coverage cutoff. This is only used for downsampling; 0 turns downsampling off. Note: It is better to slightly overestimate rather than underestimate the genome length to ensure good coverage across the genome.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
189 - config_ovl_filter_opt=--max-diff 80 --max-cov 100 --min-cov 2 --bestn 10 --min-len 4000 --gapFilt --minDepth 4 --idt-stage2 98
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
190 - max-diff : Maximum allowed difference between the coverages at the 5' and 3' ends of any particular read. If the coverage is above this value, the read is blacklisted and all of the overlaps it is incident with are ignored. If the autocompute_max_cov option is used, then the same computed value is supplied to this parameter as well.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
191 - max-cov : Maximum allowed coverage at either the 5' or the 3' end of a read. If the coverage is above this value, the read is blacklisted and all of the overlaps it is incident with are ignored. This helps remove repetitive reads which can make tangles in the string graph. Note that this value is a heuristic which works well for ~30x seed length cutoff. If the cutoff is set higher, we advise that this value be also increased. Alternatively, using the autocompute_max_cov option can automatically estimate the value of this parameter, which can improve contiguity (for example, in cases when the input genome size or the seed coverage were overestimated).
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
192 - min-cov : Minimum allowed coverage at either the 5' or the 3' end of a read. If the coverage is below this value, the read is blacklisted and all of the overlaps it is incident with are ignored. This helps remove potentially chimeric reads.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
193 - bestn : Keep at most this many overlaps on the 5' and the 3' side of any particular read
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
194 - min-len : Filter overlaps where either A-read or the B-read are shorter than this value.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
195 - gapFilt : Enables the chimera filter, which analyzes each pread's overlap pile, and determines whether a pread is chimeric based on the local coverage across the pread.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
196 - minDepth : Option for the chimera filter. The chimera filter is ignored when a local region of a read has coverage lower than this value.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
197 - idt-stage2 : Filter overlaps with identity below 98%
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
198 - config_ovl_min_idt=98 : The final overlap identity threshold. Applied during the final filtering stage, right before the overlaps are passed to the layout stage.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
199 - config_ovl_min_len=1000 : The minimum length of either A-read or a B-read to keep the overlap. Applied during the final filtering stage, right before the overlaps are passed to the layout stage.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
200 - config_ovl_opt=--one-hit-per-target --min-idt 96
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
201 - one-hit-per-target : keeps only the best hit in case there are multiple possible overlaps between a pair of reads (tandem repeats);
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
202 - min-idt : will filter out any overlap with identity lower than 96%. repeats);
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
203 - config_phase_run=1 : Enables or disables the phasing stage of the workflow. Phasing can be disabled to assemble haploid genomes, or to perform fast draft assemblies. 0 disables this feature; 1 enables it.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
204 - config_phasing_opt= : Options for the phasing tool nighthawk. The options set by this parameter are passed directly to nighthawk. For details on nighthawk options, use nighthawk -h.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
205 - config_phasing_split_opt=--split-type noverlaps --limit 3000000
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
206 - split-type : splits the chunks by the number of overlaps
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
207 - limit : allow at most approximately 3 million overlaps per chunk.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
208 - config_polish_run=1 : Enables or disables the polishing stage of the workflow. Polishing can be disabled to perform fast draft assemblies. 0 disables this feature; 1 enables it.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
209 - config_seeddb_opt=-k 30 -w 80 --space 1
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
210 - k : is the k-mer size of 30bp
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
211 - w : is the minimizer window size of 80bp;
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
212 - space : specifies the spacing for spaced seed construction, with 1 gap in between every two bases of the seed.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
213 - config_seqdb_opt=--compression 1 : Options to control the construction of the sequence database. These options are passed directly to the pancake seqdb command. Current default is --compression 1 which turns on the 2-bit encoding compression of the sequences.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
214 - config_use_hpc=0 : This parameter enables (1) or disables (0) an experimental Homopolymer Compression feature.If this feature is enabled, the overlaps are computed from homopolymer-compressed sequences. The layout stage is somewhat slower because the sequences have to be aligned to determine the correct homopolymer-expanded coordinates.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
215 - config_use_seq_ids=1 : This feature is mostly useful for debugging purposes. If 0 is specified, then the overlaps contain original sequence names instead of their numerical IDs. The default of 1 uses the numerical IDs to represent reads, which uses memory much more efficiently.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
216
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
217 *Others*
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
218
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
219 - Log: This is a basic IPA log file with the information that shows up on your terminal.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
220 - Extended log: An elaborate log file.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
221 - Config file : file containing the IPA configuration in json format
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
222
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
223 .. class:: infomark
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
224
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
225 **References**
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
226 More information are available on `GitHub <https://github.com/PacificBiosciences/pbipa/>`_.
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
227 ]]></help>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
228 <citations>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
229 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
230 author = {Ivan Sovic, Zev Kronenberg, Christopher Dunn, Derek Barnett, Sarah Kingan, James Drake},
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
231 title = {Improved Phased Assembler},
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
232 abstract = {Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with input reads and resulting in a polished assembly. IPA is fast, providing an easy to use local run mode or a distributed pipeline for a cluster},
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
233 }</citation>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
234 <citation type="bibtex">
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
235 @misc{IPA_github,
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
236 title={IPA Github page},
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
237 url = {https://github.com/PacificBiosciences/pbipa},}
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
238 </citation>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
239 </citations>
f78303e25f3e "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/ipa commit 835a903a68cae7f23fd35f3adc4af28b8f508a51"
galaxy-australia
parents:
diff changeset
240 </tool>