Mercurial > repos > richard-burhans > ncbi_egapx

comparison ncbi_egapx.xml @ 30:21d4de0e41fc 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/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bdcd7b1991f872540fb5f87ee945077b5ca68780
author richard-burhans
date Mon, 17 Feb 2025 19:17:19 +0000
parents 8ada50a892fa
children
comparison
equal deleted inserted replaced
29:8ada50a892fa 30:21d4de0e41fc
57 ]]></command> 57 ]]></command>
58 <environment_variables> 58 <environment_variables>
59 <environment_variable name="NXF_DEBUG">3</environment_variable> 59 <environment_variable name="NXF_DEBUG">3</environment_variable>
60 </environment_variables> 60 </environment_variables>
61 <configfiles> 61 <configfiles>
62 <configfile name="reads_config"><![CDATA[ 62 <configfile name="reads_config"><![CDATA[#slurp
63 #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_rnaseq_style.rnaseq_style == "history" 63 #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
64 #import re 64 #import re
65 #for $idx, $read in enumerate($cond_input_style.cond_rnaseq_style.rnaseq) 65 #for $idx, $read in enumerate($cond_input_style.cond_rnaseq_style.rnaseq)
66 #if $read 66 #if $read
67 #set $read_pathname = "reads/" + str($idx) + re.sub('[^\w\-\s]', '_', str($read.element_identifier)) + "." + $read.ext 67 #set $read_pathname = "reads/" + str($idx) + re.sub('[^\w\-\s]', '_', str($read.element_identifier)) + "." + $read.ext
80 #set $reverse_read_pathname = "reads/" + str($repeat_idx) + str($idx) + re.sub('[^\w\-\s]', '_', str($collection.reverse.element_identifier)) + "." + $collection.reverse.ext 80 #set $reverse_read_pathname = "reads/" + str($repeat_idx) + str($idx) + re.sub('[^\w\-\s]', '_', str($collection.reverse.element_identifier)) + "." + $collection.reverse.ext
81 ${repeat_idx}${idx}_${collection.name} $forward_read_pathname $reverse_read_pathname 81 ${repeat_idx}${idx}_${collection.name} $forward_read_pathname $reverse_read_pathname
82 #end for 82 #end for
83 #end for 83 #end for
84 #end if 84 #end if
85 ]]></configfile> 85 #silent pass]]></configfile>
86 <configfile name="egapx_config"><![CDATA[ 86 <configfile name="egapx_config"><![CDATA[#slurp
87 #if $cond_input_style.input_style == "fillform" 87 #if $cond_input_style.input_style == "fillform"
88 #import re 88 #import re
89 #if $cond_input_style.cond_genome_style.genome_style == "history" 89 #if $cond_input_style.cond_genome_style.genome_style == "history"
90 #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.element_identifier)) + "." + $genome.ext 90 #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.element_identifier)) + "." + $genome.ext
91 #else if $cond_input_style.cond_genome_style.genome_style == "indexed" 91 #else if $cond_input_style.cond_genome_style.genome_style == "indexed"
92 #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.fields.element_identifier)) + "." + $genomefields.ext 92 #set genome_value = "genome_" + re.sub('[^\w\-\s]', '_', str($genome.fields.element_identifier)) + "." + $genomefields.ext
93 #else 93 #else
94 #set genome_value = $uri 94 #set genome_value = $uri
95 #end if 95 #end if
96 # yaml generated by ncbi_egapx.xml 96 # yaml generated by ncbi_egapx.xml
97 genome: $genome_value 97 genome: $genome_value
98 taxid: $taxid 98 taxid: $taxid
99 #if $cond_input_style.cond_rnaseq_style.rnaseq_style == "history" 99 #if $cond_input_style.cond_rnaseq_style.rnaseq_style == "history"
100 reads: $reads_config 100 reads: $reads_config
101 #else 101 #else
102 reads: 102 reads:
103 #set reads_values = $rnaseq.split() 103 #set reads_values = $rnaseq.split()
104 #for $read in [str(rv).strip() for rv in $reads_values] 104 #for $read in [str(rv).strip() for rv in $reads_values]
105 - $read 105 - $read
106 #end for 106 #end for
107 #end if 107 #end if
108 #if str($cond_input_style.proteins) != "None" 108 #if str($cond_input_style.proteins) != "None"
109 proteins: $cond_input_style.proteins 109 proteins: $cond_input_style.proteins
110 #end if 110 #end if
111 #if str($cond_input_style.extra) != "None" 111 #if str($cond_input_style.extra) != "None"
112 #for row in str($cond_input_style.extra).strip().split("\n") 112 #for row in str($cond_input_style.extra).strip().split("\n")
113 #if $row
113 $row 114 $row
114 #end for 115 #end if
115 #end if 116 #end for
116 #end if 117 #end if
117 ]]></configfile> 118 #end if
119 #silent pass]]></configfile>
118 </configfiles> 120 </configfiles>
119 <inputs> 121 <inputs>
120 <conditional name="cond_input_style"> 122 <conditional name="cond_input_style">
121 <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?" help="Use the tool form to select inputs from the history, or use a pre-prepared yaml file."> 123 <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?" help="Use the tool form to select inputs from the history, or use a pre-prepared yaml file.">
122 <option value="fillform" selected="True">Provide configuration details for conversion into a configuration yaml</option> 124 <option value="fillform" selected="True">Provide configuration details for conversion into a configuration yaml</option>