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OpenMS place each in/output synlink in unique dir
before each symlink was placed in a dir named by the name of the corresponding parameter. this still allows for conflicts if several data sets have the sem identifier. solution: place symlinks in directory parameter_name/galaxy-dataset-id usecase: ConsensusID takes the result of different search engines for the same sample. then the identifiers of the inputs are all the sample name which leads to a conflict.
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -14,6 +14,7 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
|
@@ -32,11 +33,13 @@ mkdir out && | |
#end if | ||
#if $db.mapping: | ||
mkdir db.mapping && | ||
${ ' '.join(["ln -s '%s' 'db.mapping/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _]) } | ||
mkdir ${' '.join(["'db.mapping/%s'"%(os.path.basename(str(_))[:-4]) for _ in $db.mapping if _])} && | ||
${' '.join(["ln -s '%s' 'db.mapping/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])} | ||
#end if | ||
#if $db.struct: | ||
mkdir db.struct && | ||
${ ' '.join(["ln -s '%s' 'db.struct/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _]) } | ||
mkdir ${' '.join(["'db.struct/%s'"%(os.path.basename(str(_))[:-4]) for _ in $db.struct if _])} && | ||
${' '.join(["ln -s '%s' 'db.struct/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])} | ||
#end if | ||
## Main program call | ||
|
@@ -63,11 +66,11 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard | |
#end if | ||
#if $db.mapping: | ||
-db:mapping | ||
${' '.join(["'db.mapping/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])} | ||
${' '.join(["'db.mapping/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.mapping if _])} | ||
#end if | ||
#if $db.struct: | ||
-db:struct | ||
${' '.join(["'db.struct/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])} | ||
${' '.join(["'db.struct/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $db.struct if _])} | ||
#end if | ||
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | ||
| tee '$stdout' | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,7 +1,7 @@ | ||
<?xml version='1.0' encoding='UTF-8'?> | ||
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | ||
<!--Proposed Tool Section: [Utilities]--> | ||
<tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy1" profile="20.05"> | ||
<tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | ||
<description>Assay library generation from DDA data (Metabolomics)</description> | ||
<macros> | ||
<token name="@EXECUTABLE@">AssayGeneratorMetabo</token> | ||
|
@@ -14,12 +14,15 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | ||
mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && | ||
${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
mkdir in_id && | ||
${ ' '.join(["ln -s '%s' 'in_id/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _]) } | ||
mkdir ${' '.join(["'in_id/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_id if _])} && | ||
${' '.join(["ln -s '%s' 'in_id/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])} | ||
mkdir out && | ||
## Main program call | ||
|
@@ -29,9 +32,9 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-in | ||
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
-in_id | ||
${' '.join(["'in_id/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])} | ||
${' '.join(["'in_id/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_id if _])} | ||
-out | ||
'out/output.${out_type}' | ||
|
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---|---|---|
|
@@ -14,10 +14,12 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir cv_files && | ||
${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) } | ||
mkdir ${' '.join(["'cv_files/%s'"%(os.path.basename(str(_))[:-4]) for _ in $cv_files if _])} && | ||
${' '.join(["ln -s '%s' 'cv_files/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} | ||
#if $mapping_file: | ||
mkdir mapping_file && | ||
ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && | ||
|
@@ -33,7 +35,7 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-cv_files | ||
${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} | ||
${' '.join(["'cv_files/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} | ||
#if $mapping_file: | ||
-mapping_file | ||
'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -14,10 +14,12 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | ||
mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && | ||
${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
mkdir out && | ||
## Main program call | ||
|
@@ -27,7 +29,7 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-in | ||
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
-out | ||
'out/output.${in[0].ext}' | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -14,10 +14,12 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | ||
mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && | ||
${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
mkdir out && | ||
## Main program call | ||
|
@@ -27,7 +29,7 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-in | ||
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
-out | ||
'out/output.${gxy2omsext("fasta")}' | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -14,13 +14,16 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | ||
mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && | ||
${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
#if $in_header: | ||
mkdir in_header && | ||
${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) } | ||
mkdir ${' '.join(["'in_header/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in_header if _])} && | ||
${' '.join(["ln -s '%s' 'in_header/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} | ||
#end if | ||
mkdir pos && | ||
ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && | ||
|
@@ -36,10 +39,10 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-in | ||
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
#if $in_header: | ||
-in_header | ||
${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} | ||
${' '.join(["'in_header/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} | ||
#end if | ||
-pos | ||
'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -14,10 +14,12 @@ | |
<command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
@EXT_FOO@ | ||
#import re | ||
#import os.path | ||
## Preprocessing | ||
mkdir in && | ||
${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | ||
mkdir ${' '.join(["'in/%s'"%(os.path.basename(str(_))[:-4]) for _ in $in if _])} && | ||
${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (_, os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
#if $exp_design: | ||
mkdir exp_design && | ||
ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && | ||
|
@@ -31,7 +33,7 @@ set -o pipefail && | |
python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hardcoded_json' && | ||
@EXECUTABLE@ -ini @[email protected] | ||
-in | ||
${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
${' '.join(["'in/%s/%s.%s'"%(os.path.basename(str(_))[:-4], re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | ||
#if $exp_design: | ||
-exp_design | ||
'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' | ||
|
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