Mercurial > repos > proteore > proteore_ms_observation_pepatlas
changeset 5:034cfb96a482 draft
planemo upload commit b052261cf5cd6c2413e301a19d5c95d9794f1e81-dirty
| author | proteore |
|---|---|
| date | Wed, 13 Mar 2019 09:34:37 -0400 |
| parents | 299eb4a62e0c |
| children | e77c0f3e9bab |
| files | Get_ms-ms_observations.xml peptide_atlas.loc.sample proteore_peptide_atlas.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 26 insertions(+), 24 deletions(-) [+] |
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--- a/Get_ms-ms_observations.xml Fri Feb 01 11:48:49 2019 -0500 +++ b/Get_ms-ms_observations.xml Wed Mar 13 09:34:37 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1"> +<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26"> <description>[Peptide Atlas]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -16,7 +16,7 @@ --column_number="$input.ncol" --header="$input.header" #end if - --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])} + --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])} --output="$output" </command> @@ -41,7 +41,9 @@ <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> <!-- Peptide Atlas options -->
--- a/peptide_atlas.loc.sample Fri Feb 01 11:48:49 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -#<id> <name> <tissue> <value> -Human_Adrenal_gland_2014-08 Human Adrenal gland 2014/08 Human_Adrenal_gland tool-data/peptide_atlas/Human_Adrenal_gland_2014-08.tsv -Human_Brain_2015-01 Human Brain 2015/01 Human_Brain tool-data/peptide_atlas/Human_Brain_2015-01.tsv -Human_Breast_2014-08 Human Breast 2014/08 Human_Breast tool-data/peptide_atlas/Human_Breast_2014-08.tsv -Human_CSF_2014-09 Human CSF 2014/09 Human_CSF tool-data/peptide_atlas/Human_CSF_2014-09.tsv -Human_Colon_cancer_2013-02 Human Colon cancer 2013/02 Human_Colon_cancer tool-data/peptide_atlas/Human_Colon_cancer_2013-02.tsv -Human_Digestive_system_2014-08 Human Digestive system 2014/08 Human_Digestive_system tool-data/peptide_atlas/Human_Digestive_system_2014-08.tsv -Human_Female_reproductive_system_2014-08 Human Female reproductive system 2014/08 Human_Female_reproductive_system tool-data/peptide_atlas/Human_Female_reproductive_system_2014-08.tsv -Human_Heart_2014-08 Human Heart 2014/08 Human_Heart tool-data/peptide_atlas/Human_Heart_2014-08.tsv -Human_Kidney_2014-08 Human Kidney 2014/08 Human_Kidney tool-data/peptide_atlas/Human_Kidney_2014-08.tsv -Human_Liver_2014-08 Human Liver 2014/08 Human_Liver tool-data/peptide_atlas/Human_Liver_2014-08.tsv -Human_Lung_2014-08 Human Lung 2014/08 Human_Lung tool-data/peptide_atlas/Human_Lung_2014-08.tsv -Human_Male_reproductive_system_2014-08 Human Male reproductive system 2014/08 Human_Male_reproductive_system tool-data/peptide_atlas/Human_Male_reproductive_system_2014-08.tsv -Human_Pancreas_2014-08 Human Pancreas 2014/08 Human_Pancreas tool-data/peptide_atlas/Human_Pancreas_2014-08.tsv -Human_Plasma_non_glyco_2017-04 Human Plasma non glyco 2017/04 Human_Plasma_non_glyco tool-data/peptide_atlas/Human_Plasma_non_glyco_2017-04.tsv -Human_Spleen_2014-08 Human Spleen 2014/08 Human_Spleen tool-data/peptide_atlas/Human_Spleen_2014-08.tsv -Human_Testis_2017-01 Human Testis 2017/01 Human_Testis tool-data/peptide_atlas/Human_Testis_2017-01.tsv -Human_Urinary_bladder_2014-08 Human Urinary bladder 2014/08 Human_Urinary_bladder tool-data/peptide_atlas/Human_Urinary_bladder_2014-08.tsv -Human_Urine_2014-08 Human Urine 2014/08 Human_Urine tool-data/peptide_atlas/Human_Urine_2014-08.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_peptide_atlas.loc.sample Wed Mar 13 09:34:37 2019 -0400 @@ -0,0 +1,19 @@ +#<id> <name> <tissue> <value> +Human_Adrenal_gland_2014-08 Human Adrenal gland 2014/08 Human_Adrenal_gland tool-data/Human_Adrenal_gland_2014-08.tsv +Human_Brain_2015-01 Human Brain 2015/01 Human_Brain tool-data/Human_Brain_2015-01.tsv +Human_Breast_2014-08 Human Breast 2014/08 Human_Breast tool-data/Human_Breast_2014-08.tsv +Human_CSF_2014-09 Human CSF 2014/09 Human_CSF tool-data/Human_CSF_2014-09.tsv +Human_Colon_cancer_2013-02 Human Colon cancer 2013/02 Human_Colon_cancer tool-data/Human_Colon_cancer_2013-02.tsv +Human_Digestive_system_2014-08 Human Digestive system 2014/08 Human_Digestive_system tool-data/Human_Digestive_system_2014-08.tsv +Human_Female_reproductive_system_2014-08 Human Female reproductive system 2014/08 Human_Female_reproductive_system tool-data/Human_Female_reproductive_system_2014-08.tsv +Human_Heart_2014-08 Human Heart 2014/08 Human_Heart tool-data/Human_Heart_2014-08.tsv +Human_Kidney_2014-08 Human Kidney 2014/08 Human_Kidney tool-data/Human_Kidney_2014-08.tsv +Human_Liver_2014-08 Human Liver 2014/08 Human_Liver tool-data/Human_Liver_2014-08.tsv +Human_Lung_2014-08 Human Lung 2014/08 Human_Lung tool-data/Human_Lung_2014-08.tsv +Human_Male_reproductive_system_2014-08 Human Male reproductive system 2014/08 Human_Male_reproductive_system tool-data/Human_Male_reproductive_system_2014-08.tsv +Human_Pancreas_2014-08 Human Pancreas 2014/08 Human_Pancreas tool-data/Human_Pancreas_2014-08.tsv +Human_Plasma_non_glyco_2017-04 Human Plasma non glyco 2017/04 Human_Plasma_non_glyco tool-data/Human_Plasma_non_glyco_2017-04.tsv +Human_Spleen_2014-08 Human Spleen 2014/08 Human_Spleen tool-data/Human_Spleen_2014-08.tsv +Human_Testis_2017-01 Human Testis 2017/01 Human_Testis tool-data/Human_Testis_2017-01.tsv +Human_Urinary_bladder_2014-08 Human Urinary bladder 2014/08 Human_Urinary_bladder tool-data/Human_Urinary_bladder_2014-08.tsv +Human_Urine_2014-08 Human Urine 2014/08 Human_Urine tool-data/Human_Urine_2014-08.tsv
--- a/tool_data_table_conf.xml.sample Fri Feb 01 11:48:49 2019 -0500 +++ b/tool_data_table_conf.xml.sample Wed Mar 13 09:34:37 2019 -0400 @@ -1,8 +1,8 @@ <tables> <!-- Location of peptide reference files for proteore_ms_observation --> - <table name='peptide_atlas' comment_char="#"> + <table name='proteore_peptide_atlas' comment_char="#"> <columns>id,name,tissue,value</columns> - <file path="tool-data/peptide_atlas.loc" /> + <file path="tool-data/proteore_peptide_atlas.loc" /> </table> </tables> \ No newline at end of file