Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_data.xml @ 12:f8d3a8a2f2e5 draft

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"planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
author proteore
date Thu, 23 Jan 2020 10:44:39 +0000
parents 4c27466a4e15
children 8ee4cfdc1a92
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11:4c27466a4e15 12:f8d3a8a2f2e5
1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.22.4"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.23">
2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas] 2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.4">R</requirement> 5 <requirement type="package" version="3.4.4">R</requirement>
6 </requirements> 6 </requirements>
21 --header='$inputtype.header' 21 --header='$inputtype.header'
22 --column='$inputtype.column' 22 --column='$inputtype.column'
23 #end if 23 #end if
24 24
25 #if "protein_atlas" in str($ref_file).split("/") 25 #if "protein_atlas" in str($ref_file).split("/")
26 --hpa_ref="$ref_file" 26 --atlas="$ref_file"
27 #else 27 #else
28 --hpa_ref="$__tool_directory__/$ref_file" 28 --atlasf="$__tool_directory__/$ref_file"
29 #end if 29 #end if
30 30
31 ]]></command> 31 ]]></command>
32 32
33 <inputs> 33 <inputs>
65 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > 65 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" >
66 <option value="Gene" selected="true">Gene name</option> 66 <option value="Gene" selected="true">Gene name</option>
67 <option value="Gene description" selected="false">Gene description</option> 67 <option value="Gene description" selected="false">Gene description</option>
68 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> 68 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
69 <option value="Antibody">Antibody reference</option> 69 <option value="Antibody">Antibody reference</option>
70 <option value="RNA tissue category">RNA tissue category</option> 70 <option value="RNA tissue specificity">RNA tissue category</option>
71 <option value="Reliability (IH)">IH detection level</option> 71 <option value="Reliability (IH)">IH detection level</option>
72 <option value="Reliability (IF)">IF detection level</option> 72 <option value="Reliability (IF)">IF detection level</option>
73 <option value="Subcellular location">Subcellular location</option> 73 <option value="Subcellular location">Subcellular location</option>
74 <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> 74 <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option>
75 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> 75 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option>
76 </param> 76 </param>
77 </section> 77 </section>
78 78
79 </inputs> 79 </inputs>
80 80