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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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| 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 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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