# HG changeset patch
# User galaxyp
# Date 1372194245 14400
# Node ID 5b790728e2e29aa543f38fd6fd19c8addc5a0476
# Parent 933a77287b5f3bb6b4439d28149e19f270fa7bd6
Uploaded
diff -r 933a77287b5f -r 5b790728e2e2 idpQonvert.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpQonvert.xml Tue Jun 25 17:04:05 2013 -0400
@@ -0,0 +1,217 @@
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+ Prepare identification results for IDPicker.
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+ #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
+ #set $input_name = $input.display_name
+ #set $output_name = $input_name.split(".")[0] + ".idpDB"
+ ln -s '$input' '${input_name}';
+ ln -s '$input_database' '${db_name}';
+ idpQonvert -DecoyPrefix '${decoy_prefix}' \
+ -WriteQonversionDetails true \
+ -ProteinDatabase '${db_name}' \
+ -MaxFDR $max_fdr \
+ -EmbedSpectrumScanTimes false \
+ -EmbedSpectrumSources false \
+ #if $scoring.override_scoring
+ #set $score_info = []
+ #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
+ #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
+ #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
+ #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
+ #continue
+ #end for
+ #set $score_str = "; ".join($score_info)
+ -ScoreInfo '$score_str' \
+ #end if
+ #if $advanced_options.use_advanced_options
+ -MaxImportFDR $advanced_options.max_import_fdr \
+ -MaxResultRank $advanced_options.max_result_rank \
+ -RerankMatches $advanced_options.rerank_matches \
+ -Gamma $advanced_options.gamma \
+ -Nu $advanced_options.nu \
+ -PolynomialDegree $advanced_options.polynomial_degree \
+ -TruePositiveThreshold $advanced_options.true_positive_threshold \
+ -MaxTrainingRank $advanced_options.max_training_rank \
+ -SVMType $advanced_options.svm_type \
+ -Kernel $advanced_options.kernel \
+ -ChargeStateHandling $advanced_options.charge_state_handling \
+ -QonverterMethod $advanced_options.qonverter_method \
+ -MinPartitionSize $advanced_options.min_partition_size \
+ #end if
+ '${input_name}';
+ mv '$output_name' output
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+ idpQonvert
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+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
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+If you use this tool in Galaxy, please cite TODO
+
+
+
diff -r 933a77287b5f -r 5b790728e2e2 idpqonvert.xml
--- a/idpqonvert.xml Tue Jun 25 16:52:45 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,217 +0,0 @@
-
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- Prepare identification results for IDPicker.
-
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- #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
- #set $input_name = $input.display_name
- #set $output_name = $input_name.split(".")[0] + ".idpDB"
- ln -s '$input' '${input_name}';
- ln -s '$input_database' '${db_name}';
- idpQonvert -DecoyPrefix '${decoy_prefix}' \
- -WriteQonversionDetails true \
- -ProteinDatabase '${db_name}' \
- -MaxFDR $max_fdr \
- -EmbedSpectrumScanTimes false \
- -EmbedSpectrumSources false \
- #if $scoring.override_scoring
- #set $score_info = []
- #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
- #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
- #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
- #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
- #continue
- #end for
- #set $score_str = "; ".join($score_info)
- -ScoreInfo '$score_str' \
- #end if
- #if $advanced_options.use_advanced_options
- -MaxImportFDR $advanced_options.max_import_fdr \
- -MaxResultRank $advanced_options.max_result_rank \
- -RerankMatches $advanced_options.rerank_matches \
- -Gamma $advanced_options.gamma \
- -Nu $advanced_options.nu \
- -PolynomialDegree $advanced_options.polynomial_degree \
- -TruePositiveThreshold $advanced_options.true_positive_threshold \
- -MaxTrainingRank $advanced_options.max_training_rank \
- -SVMType $advanced_options.svm_type \
- -Kernel $advanced_options.kernel \
- -ChargeStateHandling $advanced_options.charge_state_handling \
- -QonverterMethod $advanced_options.qonverter_method \
- -MinPartitionSize $advanced_options.min_partition_size \
- #end if
- '${input_name}';
- mv '$output_name' output
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- idpQonvert
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-**What it does**
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-------
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-**Citation**
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-For the underlying tool, please cite `TODO`
-
-If you use this tool in Galaxy, please cite TODO
-
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-