Mercurial > repos > jjohnson > encyclopedia_quantify

comparison macros.xml @ 4:bd937e4efa04 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:38:25 -0400
parents aa52f0eadc85
children 30f6b9c88ceb
comparison
equal deleted inserted replaced
3:aa52f0eadc85 4:bd937e4efa04
57 #set $l_name = None 57 #set $l_name = None
58 #set $t_name = None 58 #set $t_name = None
59 </token> 59 </token>
60 60
61 <xml name="scan_input"> 61 <xml name="scan_input">
62 <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> 62 <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format">
63 <help>@MSCONVERT_RAW@</help> 63 <help>@MSCONVERT_RAW@</help>
64 </param> 64 </param>
65 </xml> 65 </xml>
66 <token name="@LINK_SCAN_INPUT@"><![CDATA[ 66 <token name="@LINK_SCAN_INPUT@"><![CDATA[
67 #set $i_name = $ln_name($i) 67 #set $i_name = $ln_name($scan_input)
68 ln -s '$i' '$i_name' && 68 ln -s '$scan_input' '$i_name' &&
69 ]]></token> 69 ]]></token>
70 <token name="@SCAN_INPUT@"> 70 <token name="@SCAN_INPUT@">
71 -i '$i_name' 71 -i '$i_name'
72 </token> 72 </token>
73 73
74 <xml name="scan_inputs"> 74 <xml name="scan_inputs">
75 <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> 75 <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">
76 <help>@MSCONVERT_RAW@</help> 76 <help>@MSCONVERT_RAW@</help>
77 </param> 77 </param>
78 </xml> 78 </xml>
79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[ 79 <token name="@LINK_SCAN_INPUTS@"><![CDATA[
80 #set $inputs_dir = 'inputs' 80 #set $inputs_dir = 'inputs'
81 mkdir -p $inputs_dir && 81 mkdir -p $inputs_dir &&
82 #for $sf in $i 82 #for $sf in $scan_inputs
83 #set $i_name = $ln_name($sf) 83 #set $i_name = $ln_name($sf)
84 ln -s '$sf' '${inputs_dir}/${i_name}' && 84 ln -s '$sf' '${inputs_dir}/${i_name}' &&
85 #end for 85 #end for
86 ]]></token> 86 ]]></token>
87 <token name="@SCAN_INPUTS@"> 87 <token name="@SCAN_INPUTS@">
88 -i '$inputs_dir' 88 -i '$inputs_dir'
89 </token> 89 </token>
90 90
91 <xml name="fasta_input"> 91 <xml name="fasta_input">
92 <param argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> 92 <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database">
93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> 93 <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>
94 </param> 94 </param>
95 </xml> 95 </xml>
96 <token name="@LINK_FASTA_INPUT@"><![CDATA[ 96 <token name="@LINK_FASTA_INPUT@"><![CDATA[
97 #set $f_name = $ln_name($f) 97 #set $f_name = $ln_name($fasta)
98 ln -s '$f' '$f_name' && 98 ln -s '$fasta' '$f_name' &&
99 ]]></token> 99 ]]></token>
100 <token name="@FASTA_INPUT@"> 100 <token name="@FASTA_INPUT@">
101 -f '$f_name' 101 -f '$f_name'
102 </token> 102 </token>
103 103
104 <xml name="target_fasta"> 104 <xml name="target_fasta">
105 <param argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> 105 <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/>
106 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> 106 <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
107 </xml> 107 </xml>
108 <token name="@LINK_TARGET_FASTA@"><![CDATA[ 108 <token name="@LINK_TARGET_FASTA@"><![CDATA[
109 #if $t 109 #if $target_fasta
110 #set $t_name = $ln_name($t) 110 #set $t_name = $ln_name($target_fasta)
111 ln -s '$t' '$t_name' && 111 ln -s '$target_fasta' '$t_name' &&
112 #else 112 #else
113 #set $t_name = None 113 #set $t_name = None
114 #end if 114 #end if
115 ]]></token> 115 ]]></token>
116 <token name="@TARGET_FASTA@"> 116 <token name="@TARGET_FASTA@">
119 -tp $tp 119 -tp $tp
120 #end if 120 #end if
121 </token> 121 </token>
122 122
123 <xml name="lib_input" token_optional="true" token_libhelp=""> 123 <xml name="lib_input" token_optional="true" token_libhelp="">
124 <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> 124 <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB">
125 <help>@LIBHELP@</help> 125 <help>@LIBHELP@</help>
126 </param> 126 </param>
127 </xml> 127 </xml>
128 <token name="@LINK_LIB_INPUT@"><![CDATA[ 128 <token name="@LINK_LIB_INPUT@"><![CDATA[
129 #if $l 129 #if $library
130 #set $l_name = $ln_name($l) 130 #set $l_name = $ln_name($library)
131 cp '$l' $l_name && 131 cp '$library' $l_name &&
132 #else 132 #else
133 #set $l_name = None 133 #set $l_name = None
134 #end if 134 #end if
135 ]]></token> 135 ]]></token>
136 <token name="@LIB_INPUT@"> 136 <token name="@LIB_INPUT@">