Mercurial > repos > bgruening > instagraal

comparison instagraal.xml @ 2:d1be552c6034 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/bgruening/galaxytools/tree/master/tools/instagraal commit c5ff906bec1f07b06a60081f7db3fc8f0c6e94b8
author bgruening
date Sun, 27 Aug 2023 09:28:26 +0000
parents 8d5b13b571fd
children
comparison
equal deleted inserted replaced
1:8d5b13b571fd 2:d1be552c6034
1 <tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="instagraal" name="instaGRAAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>Large genome reassembly based on Hi-C data</description> 2 <description>Large genome reassembly based on Hi-C data</description>
3 <xrefs>
4 <xref type="bio.tools">instagraal</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">0.1.6</token> 7 <token name="@TOOL_VERSION@">0.1.6</token>
5 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 9 </macros>
7 <xrefs> 10 <requirements>
8 <xref type="bio.tools">instagraal</xref> 11 <!-- use a versioned copy of the upstream container at koszullab/instagraal -->
9 </xrefs> 12 <container type="docker">quay.io/galaxy/instagraal:0.1.6</container>
13 <resource type="cuda_version_min">10.0</resource>
14 <resource type="cuda_compute_capability">3.0</resource>
15 <resource type="cuda_device_count_min">1</resource>
16 </requirements>
10 <stdio> 17 <stdio>
11 <regex match="instagraal_class" level="warning" description="instaGRAAL is raining an expected error at the end."/> 18 <regex match="instagraal_class" level="warning" description="instaGRAAL is raining an expected error at the end."/>
12 <regex match="Exception:"/> 19 <regex match="Exception:"/>
13 <exit_code range="2:"/> 20 <exit_code range="2:"/>
14 <exit_code range=":-1"/> 21 <exit_code range=":-1"/>
15 </stdio> 22 </stdio>
16 <requirements>
17 <container type="docker">koszullab/instagraal</container>
18 </requirements>
19 <version_command>instagraal --version</version_command> 23 <version_command>instagraal --version</version_command>
20 <command> 24 <command>
21 <![CDATA[ 25 <![CDATA[
22 26
23 #set gap_string = 'N' * int($number_of_n) 27 #set gap_string = 'N' * int($number_of_n)
94 <param argument="--coverage-std" type="integer" value="1" min="0" max="1" label="Number of standard deviations below the mean" 98 <param argument="--coverage-std" type="integer" value="1" min="0" max="1" label="Number of standard deviations below the mean"
95 help="Coverage below which fragments should be filtered out prior to binning." /> 99 help="Coverage below which fragments should be filtered out prior to binning." />
96 100
97 <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" /> 101 <param argument="--neighborhood" type="integer" value="5" min="0" max="100" label="Number of neighbors to sample for potential mutations for each bin" />
98 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" /> 102 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Indicates genome is circular" />
99 <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Indicates genome is circular" />
100 <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" /> 103 <param argument="--bomb" type="boolean" truevalue="--bomb" falsevalue="" label="Explode the genome prior to scaffolding" />
101 <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" /> 104 <param argument="--pyramid-only" type="boolean" truevalue="--pyramid-only" falsevalue="" label="Only build multi-resolution contact maps (pyramids) and don't do any scaffolding" />
102 <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" /> 105 <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" label="Only perform operations at the edge of the contigs" />
103 <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step" /> 106 <param name="number_of_n" type="integer" value="10" min="1" label="Number of Ns that you want to include during the polishing step" />
104 107
105 </inputs> 108 </inputs>
106 <outputs> 109 <outputs>
107 <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta"/> 110 <data name="genome" format="fasta" from_work_dir="./outputs/genome.fasta" label="${tool.name} on ${on_string}: Genome sequence"/>
108 <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt"/> 111 <data name="frags" format="tabular" from_work_dir="./outputs/info_frags.txt" label="${tool.name} on ${on_string}: Fragment information"/>
109 <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta"/> 112 <data name="curated" format="fasta" from_work_dir="./outputs/curated.fasta" label="${tool.name} on ${on_string}: Curated sequences"/>
110 </outputs> 113 </outputs>
111 <tests> 114 <tests>
112 <test> 115 <test>
113 <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" /> 116 <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
114 <param name="fragments_list" value="fragments_list.tabular" /> 117 <param name="fragments_list" value="fragments_list.tabular" />