Mercurial > repos > iuc > semibin_generate_cannot_links

comparison generate_cannot_links.xml @ 3:68d2cd0be567 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:53:41 +0000
parents a6f004bc73bf
children
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2:a6f004bc73bf 3:68d2cd0be567
16 --input-fasta 'contigs.fasta' 16 --input-fasta 'contigs.fasta'
17 --output 'output' 17 --output 'output'
18 --cannot-name 'cannot' 18 --cannot-name 'cannot'
19 #if $mode.ref.select == "cached" 19 #if $mode.ref.select == "cached"
20 --reference-db-data-dir '$mode.ref.cached_db.fields.path' 20 --reference-db-data-dir '$mode.ref.cached_db.fields.path'
21 #else 21 #end if
22 #if $mode.ref.select == "taxonomy"
22 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table' 23 --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
23 #end if 24 #end if
24 @MIN_LEN@ 25 @MIN_LEN@
25 #if str($ml_threshold) != '' 26 #if $ml_threshold:
26 --ml-threshold $ml_threshold 27 --ml-threshold $ml_threshold
27 #end if 28 #end if
28 --cannot-name 'cannot' 29 --cannot-name 'cannot'
29 --threads \${GALAXY_SLOTS:-1} 30 --threads \${GALAXY_SLOTS:-1}
30 --processes \${GALAXY_SLOTS:-1} 31 --processes \${GALAXY_SLOTS:-1}
32 <inputs> 33 <inputs>
33 <conditional name="mode"> 34 <conditional name="mode">
34 <expand macro="mode_select"/> 35 <expand macro="mode_select"/>
35 <when value="single"> 36 <when value="single">
36 <expand macro="input-fasta-single"/> 37 <expand macro="input-fasta-single"/>
37 <expand macro="ref-single"/> 38 <expand macro="ref-single-cannot"/>
38 </when> 39 </when>
39 <when value="co"> 40 <when value="co">
40 <expand macro="input-fasta-single"/> 41 <expand macro="input-fasta-single"/>
41 <expand macro="ref-single"/> 42 <expand macro="ref-single-cannot"/>
42 </when> 43 </when>
43 <when value="multi"> 44 <when value="multi">
44 <expand macro="input-fasta-multi"/> 45 <expand macro="input-fasta-multi"/>
45 <expand macro="ref-multi"/> 46 <expand macro="ref-multi-cannot"/>
46 </when> 47 </when>
47 </conditional> 48 </conditional>
48 <expand macro="min_len"/> 49 <expand macro="min_len"/>
49 <expand macro="ml-threshold"/> 50 <expand macro="ml-threshold"/>
50 </inputs> 51 </inputs>
63 </conditional> 64 </conditional>
64 <conditional name="min_len"> 65 <conditional name="min_len">
65 <param name="method" value="min-len"/> 66 <param name="method" value="min-len"/>
66 <param name="min_len" value="0" /> 67 <param name="min_len" value="0" />
67 </conditional> 68 </conditional>
68 <param name="ml_threshold" value=""/>
69 <output name="cannot" ftype="txt"> 69 <output name="cannot" ftype="txt">
70 <assert_contents> 70 <assert_contents>
71 <has_text text="g1k_0,g4k_0"/> 71 <has_text text="g1k_0,g4k_0"/>
72 <has_text text="g2k_3,g4k_5"/> 72 <has_text text="g2k_3,g4k_5"/>
73 <has_text text="g4k_6,g4k_5"/> 73 <has_text text="g4k_6,g4k_5"/>
85 </conditional> 85 </conditional>
86 <conditional name="min_len"> 86 <conditional name="min_len">
87 <param name="method" value="min-len"/> 87 <param name="method" value="min-len"/>
88 <param name="min_len" value="0" /> 88 <param name="min_len" value="0" />
89 </conditional> 89 </conditional>
90 <param name="ml_threshold" value=""/>
91 <output name="cannot" ftype="txt"> 90 <output name="cannot" ftype="txt">
92 <assert_contents> 91 <assert_contents>
93 <has_text text="g1k_0,g4k_0"/> 92 <has_text text="g1k_0,g4k_0"/>
94 <has_text text="g2k_3,g4k_5"/> 93 <has_text text="g2k_3,g4k_5"/>
95 <has_text text="g4k_6,g4k_5"/> 94 <has_text text="g4k_6,g4k_5"/>
99 <test expect_num_outputs="1"> 98 <test expect_num_outputs="1">
100 <conditional name="mode"> 99 <conditional name="mode">
101 <param name="select" value="single"/> 100 <param name="select" value="single"/>
102 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 101 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
103 <conditional name="ref"> 102 <conditional name="ref">
104 <param name="db_selector" value="cached"/> 103 <param name="select" value="cached"/>
105 <param name="cached_db" value="test-db"/> 104 <param name="cached_db" value="test-db"/>
106 </conditional> 105 </conditional>
107 </conditional> 106 </conditional>
108 <conditional name="min_len"> 107 <conditional name="min_len">
109 <param name="method" value="min-len"/> 108 <param name="method" value="min-len"/>
110 <param name="min_len" value="0" /> 109 <param name="min_len" value="0" />
111 </conditional> 110 </conditional>
112 <param name="ml_threshold" value=""/>
113 <output name="cannot" ftype="txt"> 111 <output name="cannot" ftype="txt">
114 <assert_contents> 112 <assert_contents>
115 <has_text text="g1k_0,g2k_0"/> 113 <has_n_lines n='300' delta="10"/>
116 <has_text text="g2k_9,g4k_1"/>
117 </assert_contents> 114 </assert_contents>
118 </output> 115 </output>
119 </test> 116 </test>
120 </tests> 117 </tests>
121 <help><![CDATA[ 118 <help><![CDATA[