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comparison cactus_export.xml @ 15:c44f824c051a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
author iuc
date Thu, 08 Feb 2024 08:52:41 +0000
parents d7ce0ec78e51
children
comparison
equal deleted inserted replaced
14:3ff17bad4006 15:c44f824c051a
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&
10 9
11 ## check if the reference level was specified 10 ## check if the reference level was specified
12 #if $export_select.format in ['maf_selector', 'vg_selector']: 11 #if $export_select.format in ['maf_selector', 'vg_selector']:
13 #if $export_select.ref_level == '': 12 #if $export_select.ref_level == '':
14 echo "You must provide a reference level" && 13 echo "You must provide a reference level" &&
15 exit 1 14 exit 1 ;
16 #end if 15 #end if
17 #end if 16 #end if
18 17
19 ln -s '$hal_file' alignment.hal 18 ln -s '$hal_file' alignment.hal
20 19
30 ## make an assemblyHub 29 ## make an assemblyHub
31 #if $export_select.format == 'ah_selector': 30 #if $export_select.format == 'ah_selector':
32 && 31 &&
33 hal2assemblyHub.py 32 hal2assemblyHub.py
34 --maxCores \${GALAXY_SLOTS:-4} 33 --maxCores \${GALAXY_SLOTS:-4}
35 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 34 --maxMemory \${GALAXY_MEMORY_MB:-8196}M
36 ./jobStore 35 ./jobStore
37 alignment.hal 36 alignment.hal
38 assemblyhub 37 assemblyhub
39 && 38 &&
40 tar -cv assemblyhub > assemblyhub.tar 39 tar -cv assemblyhub > assemblyhub.tar
48 > alignment.pg 47 > alignment.pg
49 #end if 48 #end if
50 49
51 ]]></command> 50 ]]></command>
52 <inputs> 51 <inputs>
53 <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus" /> 52 <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus"/>
54 <conditional name="export_select"> 53 <conditional name="export_select">
55 <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format."> 54 <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format.">
56 <option value="maf_selector" selected="true">MAF file</option> 55 <option value="maf_selector" selected="true">MAF file</option>
57 <option value="ah_selector">Assembly Hub</option> 56 <option value="ah_selector">Assembly Hub</option>
58 <option value="vg_selector">VG file</option> 57 <option value="vg_selector">VG file</option>
59 </param> 58 </param>
60 <when value="maf_selector"> 59 <when value="maf_selector">
61 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." /> 60 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
62 </when> 61 </when>
63 <when value="ah_selector"> 62 <when value="ah_selector">
64 </when> 63 </when>
65 <when value="vg_selector"> 64 <when value="vg_selector">
66 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." /> 65 <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
67 </when> 66 </when>
68 </conditional> 67 </conditional>
69 </inputs> 68 </inputs>
70 <outputs> 69 <outputs>
71 <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)" > 70 <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)">
72 <filter>export_select['format'] == 'maf_selector'</filter> 71 <filter>export_select['format'] == 'maf_selector'</filter>
73 </data> 72 </data>
74 <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)" > 73 <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)">
75 <filter>export_select['format'] == 'vg_selector'</filter> 74 <filter>export_select['format'] == 'vg_selector'</filter>
76 </data> 75 </data>
77 <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)" > 76 <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)">
78 <filter>export_select['format'] == 'ah_selector'</filter> 77 <filter>export_select['format'] == 'ah_selector'</filter>
79 </data> 78 </data>
80 </outputs> 79 </outputs>
81 <tests> 80 <tests>
82 <!-- this fails because no reference level is set --> 81 <!-- this fails because no reference level is set -->
83 <test expect_failure="true"> 82 <test expect_failure="true">
84 <conditional name="export_select"> 83 <conditional name="export_select">
85 <param name="format" value="maf_selector" /> 84 <param name="format" value="maf_selector"/>
86 </conditional> 85 </conditional>
87 <param name="hal_file" ftype="h5" value="evolverMammals.hal" /> 86 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals.hal"/>
88 </test> 87 </test>
89 <!-- within-species mode --> 88 <!-- within-species mode -->
90 <test expect_num_outputs="1"> 89 <test expect_num_outputs="1">
91 <conditional name="export_select"> 90 <conditional name="export_select">
92 <param name="ref_level" value="simMouse_chr6" /> 91 <param name="ref_level" value="simMouse_chr6"/>
93 <param name="format" value="maf_selector" /> 92 <param name="format" value="maf_selector"/>
94 </conditional> 93 </conditional>
95 <param name="hal_file" ftype="h5" value="within.hal" /> 94 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
96 <output name="out_maf" file="set_reference.maf" /> 95 <output name="out_maf" location="https://zenodo.org/record/8336793/files/set_reference.maf"/>
97 </test> 96 </test>
98 <!-- between-species --> 97 <!-- between-species -->
99 <test expect_num_outputs="1"> 98 <test expect_num_outputs="1">
100 <conditional name="export_select"> 99 <conditional name="export_select">
101 <param name="ref_level" value="simMouse_chr6" /> 100 <param name="ref_level" value="simMouse_chr6"/>
102 <param name="format" value="maf_selector" /> 101 <param name="format" value="maf_selector"/>
103 </conditional> 102 </conditional>
104 <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" /> 103 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.hal"/>
105 <output name="out_maf" file="evolverMammals_noroot.maf" /> 104 <output name="out_maf" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.maf"/>
106 </test> 105 </test>
107 <!-- assembly hub format --> 106 <!-- assembly hub format -->
108 <test expect_num_outputs="1"> 107 <test expect_num_outputs="1">
109 <conditional name="export_select"> 108 <conditional name="export_select">
110 <param name="format" value="ah_selector" /> 109 <param name="format" value="ah_selector"/>
111 </conditional> 110 </conditional>
112 <param name="hal_file" ftype="h5" value="within.hal" /> 111 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
113 <output name="out_ah"> 112 <output name="out_ah">
114 <assert_contents> 113 <assert_contents>
115 <has_archive_member path="assemblyhub/hub.txt"/> 114 <has_archive_member path="assemblyhub/hub.txt"/>
116 </assert_contents> 115 </assert_contents>
117 </output> 116 </output>
118 </test> 117 </test>
119 <!-- vg format --> 118 <!-- vg format -->
120 <test expect_num_outputs="1"> 119 <test expect_num_outputs="1">
121 <conditional name="export_select"> 120 <conditional name="export_select">
122 <param name="format" value="vg_selector" /> 121 <param name="format" value="vg_selector"/>
123 <param name="ref_level" value="simMouse_chr6" /> 122 <param name="ref_level" value="simMouse_chr6"/>
124 </conditional> 123 </conditional>
125 <param name="hal_file" ftype="h5" value="within.hal" /> 124 <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
126 <output name="out_vg"> 125 <output name="out_vg">
127 <assert_contents> 126 <assert_contents>
128 <has_size value="860452" delta="200000" /> 127 <has_size value="860452" delta="200000"/>
129 </assert_contents> 128 </assert_contents>
130 </output> 129 </output>
131 </test> 130 </test>
132 <!-- gfa format (gfa2): not implemented --> 131 <!-- gfa format (gfa2): not implemented -->
133 </tests> 132 </tests>