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P2m2tools docker env #26

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P2m2tools docker env #26

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6bcf594
update gcms
ofilangi Nov 5, 2021
2a3befe
Merge pull request #1 from p2m2/openlabcds2csv
ofilangi Nov 5, 2021
491e6ef
Merge branch 'master' of https://github.com/genouest/galaxy-tools
ofilangi Nov 5, 2021
d2ee00b
update xml gcms2isocor, openlabcds2csv using docker container. remove…
ofilangi Nov 8, 2021
7f1ce39
add link to url repo p2m2tools. remove profile version
ofilangi Nov 8, 2021
13aa266
add link to url repo p2m2tools. remove profile version
ofilangi Nov 8, 2021
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Binary file removed tools/gcms2isocor/P2M2WorkflowsTools-assembly-0.1.jar
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11 changes: 11 additions & 0 deletions tools/gcms2isocor/README.md
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### dev notes

## repo

https://github.com/p2m2/p2m2tools

## planemo

planemo l --report_level error
planemo t --docker

10 changes: 6 additions & 4 deletions tools/gcms2isocor/gcms2isocor.xml
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<tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="0.1.0" profile="20.09">
<requirements>
<requirement type="package" version="8.0.121">openjdk</requirement>
<tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" version="1.0.0">
<requirements>
<container type="docker">inraep2m2/p2m2tools:0.1.5</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
java -jar '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.jar'
p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand
#for $input in $input_gcms_files
#if $input
$input
Expand Down Expand Up @@ -33,5 +33,7 @@

Example: the name “ProlineC2C5_TMS_m0” is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue
monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146).

Questions, suggestions or bugs report, please submit an issue at https://github.com/p2m2/p2m2tools/issues/new?labels=bug&title=[GCMS2IsocorCommand].
]]></help>
</tool>
Binary file removed tools/openlabcds2csv/P2M2WorkflowsTools-assembly-0.1.4.jar
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17 changes: 6 additions & 11 deletions tools/openlabcds2csv/README.md
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### generation avec planemo
### dev notes

```
cp ../../target/scala-2.13/P2M2WorkflowsTools-assembly-*.jar .
```
## repo

dans openlabcds2csv.xml balise <command>
https://github.com/p2m2/p2m2tools

`openlabcds2csv` doit etre remplacer par `java -jar '$__tool_directory__/P2M2WorkflowsTools-assembly-xxxx.jar'`
## planemo

planemo l
planemo t
planemo l --report_level error
planemo t --docker

### todo

paquet bioconda
12 changes: 7 additions & 5 deletions tools/openlabcds2csv/openlabcds2csv.xml
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<tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" version="0.1.0" profile="20.09">
<requirements>
<requirement type="package" version="8.0.121">openjdk</requirement>
<tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" version="1.0.0">
<requirements>
<container type="docker">inraep2m2/p2m2tools:0.1.5</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
java -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.OpenLabCDS2CsvCommand
p2m2tools fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand
#for $input in $input_openlabscds_files
#if $input
$input
Expand Down Expand Up @@ -35,6 +35,8 @@
</tests>
<help><![CDATA[
Get multiple "Internal Standard Report" from the OpenLabCDS software where are describe a list of compound in format row (columns : RetTime Type ISTD Area Amt/Area Amount Grp Name)
The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values ​​for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name)
The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values ​​for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name).

Questions, suggestions or bugs report, please submit an issue at https://github.com/p2m2/p2m2tools/issues/new?labels=bug&title=[OpenLabCDS2CsvCommand].
]]></help>
</tool>