Mercurial > repos > galaxyp > pepquery2_index
comparison macros.xml @ 1:494b670f336d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
| author | galaxyp |
|---|---|
| date | Sun, 02 Oct 2022 23:50:53 +0000 |
| parents | e9ef3add4ca8 |
| children |
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| 0:e9ef3add4ca8 | 1:494b670f336d |
|---|---|
| 64 #end for | 64 #end for |
| 65 pepquery index -i input_dir -o index_dir | 65 pepquery index -i input_dir -o index_dir |
| 66 #end def | 66 #end def |
| 67 ]]></token> | 67 ]]></token> |
| 68 | 68 |
| 69 <xml name="pepquerydb_options"> | |
| 70 <option value="all">all</option> | |
| 71 <option value="w">w:global proteome</option> | |
| 72 <option value="p">p:phosphorylation</option> | |
| 73 <option value="a">a:acetylation</option> | |
| 74 <option value="u">u:ubiquitination</option> | |
| 75 <option value="g">g:glycosylation</option> | |
| 76 <option value="Academia_Sinica_LUAD100_Phosphoproteome_PDC000220">Academia_Sinica_LUAD100_Phosphoproteome_PDC000220</option> | |
| 77 <option value="Academia_Sinica_LUAD100_Proteome_PDC000219">Academia_Sinica_LUAD100_Proteome_PDC000219</option> | |
| 78 <option value="CCLE_proteome_MSV000085836">CCLE_proteome_MSV000085836</option> | |
| 79 <option value="CPTAC">CPTAC</option> | |
| 80 <option value="CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128">CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128</option> | |
| 81 <option value="CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127">CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127</option> | |
| 82 <option value="CPTAC_GBM_Discovery_Study_Acetylome_PDC000245">CPTAC_GBM_Discovery_Study_Acetylome_PDC000245</option> | |
| 83 <option value="CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205">CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205</option> | |
| 84 <option value="CPTAC_GBM_Discovery_Study_Proteome_PDC000204">CPTAC_GBM_Discovery_Study_Proteome_PDC000204</option> | |
| 85 <option value="CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222">CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222</option> | |
| 86 <option value="CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221">CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221</option> | |
| 87 <option value="CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233">CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233</option> | |
| 88 <option value="CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232">CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232</option> | |
| 89 <option value="CPTAC_LSCC_Discovery_Study_Proteome_PDC000234">CPTAC_LSCC_Discovery_Study_Proteome_PDC000234</option> | |
| 90 <option value="CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237">CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237</option> | |
| 91 <option value="CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224">CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224</option> | |
| 92 <option value="CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149">CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149</option> | |
| 93 <option value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153">CPTAC_LUAD_Discovery_Study_Proteome_PDC000153</option> | |
| 94 <option value="CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271">CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271</option> | |
| 95 <option value="CPTAC_PDA_Discovery_Study_Proteome_PDC000270">CPTAC_PDA_Discovery_Study_Proteome_PDC000270</option> | |
| 96 <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176</option> | |
| 97 <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180</option> | |
| 98 <option value="CPTAC_Prospective_Breast_BI_Acetylome_PDC000239">CPTAC_Prospective_Breast_BI_Acetylome_PDC000239</option> | |
| 99 <option value="CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121">CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121</option> | |
| 100 <option value="CPTAC_Prospective_Breast_BI_Proteome_PDC000120">CPTAC_Prospective_Breast_BI_Proteome_PDC000120</option> | |
| 101 <option value="CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117">CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117</option> | |
| 102 <option value="CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116">CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116</option> | |
| 103 <option value="CPTAC_Prospective_Colon_VU_Proteome_PDC000109">CPTAC_Prospective_Colon_VU_Proteome_PDC000109</option> | |
| 104 <option value="CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251">CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251</option> | |
| 105 <option value="CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110">CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110</option> | |
| 106 <option value="CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119">CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119</option> | |
| 107 <option value="CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118">CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118</option> | |
| 108 <option value="CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174">CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174</option> | |
| 109 <option value="CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173">CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173</option> | |
| 110 <option value="CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111">CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111</option> | |
| 111 <option value="CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112">CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112</option> | |
| 112 <option value="CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115">CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115</option> | |
| 113 <option value="CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114">CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114</option> | |
| 114 <option value="CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226">CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226</option> | |
| 115 <option value="CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126">CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126</option> | |
| 116 <option value="CPTAC_UCEC_Discovery_Study_Proteome_PDC000125">CPTAC_UCEC_Discovery_Study_Proteome_PDC000125</option> | |
| 117 <option value="Deep_29_healthy_human_tissues_PXD010154">Deep_29_healthy_human_tissues_PXD010154</option> | |
| 118 <option value="GTEx_32_Tissues_Proteome_PXD016999">GTEx_32_Tissues_Proteome_PXD016999</option> | |
| 119 <option value="HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199">HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199</option> | |
| 120 <option value="HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198">HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198</option> | |
| 121 <option value="Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262">Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262</option> | |
| 122 <option value="Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216">Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216</option> | |
| 123 <option value="Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215">Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215</option> | |
| 124 <option value="Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214">Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214</option> | |
| 125 </xml> | |
| 69 | 126 |
| 70 <xml name="modifications"> | 127 <xml name="modifications"> |
| 71 <option value="0">0: NO Modifications</option> | 128 <option value="0">0: NO Modifications</option> |
| 72 <option value="1">1: Carbamidomethylation of C [57.02146372057]</option> | 129 <option value="1">1: Carbamidomethylation of C [57.02146372057]</option> |
| 73 <option value="2">2: Oxidation of M [15.99491461956]</option> | 130 <option value="2">2: Oxidation of M [15.99491461956]</option> |