mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merged in trevorw/galaxy-central (pull request #3)
This commit is contained in:
James Taylor
@@ -123,7 +123,7 @@
|
||||
<datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true">
|
||||
<converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/>
|
||||
<converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
|
||||
<converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
|
||||
<converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
|
||||
</datatype>
|
||||
<datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
|
||||
<datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/>
|
||||
@@ -274,10 +274,10 @@
|
||||
</registration>
|
||||
<sniffers>
|
||||
<!--
|
||||
The order in which Galaxy attempts to determine data types is
|
||||
important because some formats are much more loosely defined
|
||||
than others. The following list should be the most rigidly
|
||||
defined format first, followed by next-most rigidly defined,
|
||||
The order in which Galaxy attempts to determine data types is
|
||||
important because some formats are much more loosely defined
|
||||
than others. The following list should be the most rigidly
|
||||
defined format first, followed by next-most rigidly defined,
|
||||
and so on.
|
||||
-->
|
||||
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
|
||||
|
||||
+12
-12
@@ -51,7 +51,7 @@
|
||||
<tool file="fasta_tools/fasta_to_tabular.xml" />
|
||||
<tool file="filters/gff2bed.xml" />
|
||||
<tool file="maf/maf_to_bed.xml" />
|
||||
<tool file="maf/maf_to_interval.xml" />
|
||||
<tool file="maf/maf_to_interval.xml" />
|
||||
<tool file="maf/maf_to_fasta.xml" />
|
||||
<tool file="fasta_tools/tabular_to_fasta.xml" />
|
||||
<tool file="fastq/fastq_to_fasta.xml" />
|
||||
@@ -78,13 +78,13 @@
|
||||
<tool file="filters/gff/extract_GFF_Features.xml" />
|
||||
<tool file="filters/gff/gff_filter_by_attribute.xml" />
|
||||
<tool file="filters/gff/gff_filter_by_feature_count.xml" />
|
||||
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
|
||||
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
|
||||
</section>
|
||||
<section name="Join, Subtract and Group" id="group">
|
||||
<tool file="filters/joiner.xml" />
|
||||
<tool file="filters/compare.xml"/>
|
||||
<tool file="new_operations/subtract_query.xml"/>
|
||||
<tool file="stats/grouping.xml" />
|
||||
<tool file="stats/grouping.xml" />
|
||||
<tool file="new_operations/column_join.xml"/>
|
||||
</section>
|
||||
<section name="Extract Features" id="features">
|
||||
@@ -112,7 +112,7 @@
|
||||
<tool file="extract/phastOdds/phastOdds_tool.xml" />
|
||||
</section>
|
||||
<section name="Operate on Genomic Intervals" id="bxops">
|
||||
<tool file="new_operations/intersect.xml" />
|
||||
<tool file="new_operations/intersect.xml" />
|
||||
<tool file="new_operations/subtract.xml" />
|
||||
<tool file="new_operations/merge.xml" />
|
||||
<tool file="new_operations/concat.xml" />
|
||||
@@ -127,7 +127,7 @@
|
||||
</section>
|
||||
<section name="Statistics" id="stats">
|
||||
<tool file="stats/gsummary.xml" />
|
||||
<tool file="filters/uniq.xml" />
|
||||
<tool file="filters/uniq.xml" />
|
||||
<tool file="stats/cor.xml" />
|
||||
<tool file="stats/generate_matrix_for_pca_lda.xml" />
|
||||
<tool file="stats/lda_analy.xml" />
|
||||
@@ -223,13 +223,13 @@
|
||||
<tool file="emboss_5/emboss_chips.xml" />
|
||||
<tool file="emboss_5/emboss_cirdna.xml" />
|
||||
<tool file="emboss_5/emboss_codcmp.xml" />
|
||||
<tool file="emboss_5/emboss_coderet.xml" />
|
||||
<tool file="emboss_5/emboss_coderet.xml" />
|
||||
<tool file="emboss_5/emboss_compseq.xml" />
|
||||
<tool file="emboss_5/emboss_cpgplot.xml" />
|
||||
<tool file="emboss_5/emboss_cpgplot.xml" />
|
||||
<tool file="emboss_5/emboss_cpgreport.xml" />
|
||||
<tool file="emboss_5/emboss_cusp.xml" />
|
||||
<tool file="emboss_5/emboss_cutseq.xml" />
|
||||
<tool file="emboss_5/emboss_dan.xml" />
|
||||
<tool file="emboss_5/emboss_dan.xml" />
|
||||
<tool file="emboss_5/emboss_degapseq.xml" />
|
||||
<tool file="emboss_5/emboss_descseq.xml" />
|
||||
<tool file="emboss_5/emboss_diffseq.xml" />
|
||||
@@ -245,7 +245,7 @@
|
||||
<tool file="emboss_5/emboss_etandem.xml" />
|
||||
<tool file="emboss_5/emboss_extractfeat.xml" />
|
||||
<tool file="emboss_5/emboss_extractseq.xml" />
|
||||
<tool file="emboss_5/emboss_freak.xml" />
|
||||
<tool file="emboss_5/emboss_freak.xml" />
|
||||
<tool file="emboss_5/emboss_fuzznuc.xml" />
|
||||
<tool file="emboss_5/emboss_fuzzpro.xml" />
|
||||
<tool file="emboss_5/emboss_fuzztran.xml" />
|
||||
@@ -266,7 +266,7 @@
|
||||
<tool file="emboss_5/emboss_merger.xml" />
|
||||
<tool file="emboss_5/emboss_msbar.xml" />
|
||||
<tool file="emboss_5/emboss_needle.xml" />
|
||||
<tool file="emboss_5/emboss_newcpgreport.xml" />
|
||||
<tool file="emboss_5/emboss_newcpgreport.xml" />
|
||||
<tool file="emboss_5/emboss_newcpgseek.xml" />
|
||||
<tool file="emboss_5/emboss_newseq.xml" />
|
||||
<tool file="emboss_5/emboss_noreturn.xml" />
|
||||
@@ -294,7 +294,7 @@
|
||||
<tool file="emboss_5/emboss_revseq.xml" />
|
||||
<tool file="emboss_5/emboss_seqmatchall.xml" />
|
||||
<tool file="emboss_5/emboss_seqret.xml" />
|
||||
<tool file="emboss_5/emboss_showfeat.xml" />
|
||||
<tool file="emboss_5/emboss_showfeat.xml" />
|
||||
<tool file="emboss_5/emboss_shuffleseq.xml" />
|
||||
<tool file="emboss_5/emboss_sigcleave.xml" />
|
||||
<tool file="emboss_5/emboss_sirna.xml" />
|
||||
@@ -316,7 +316,7 @@
|
||||
<tool file="emboss_5/emboss_water.xml" />
|
||||
<tool file="emboss_5/emboss_wobble.xml" />
|
||||
<tool file="emboss_5/emboss_wordcount.xml" />
|
||||
<tool file="emboss_5/emboss_wordmatch.xml" />
|
||||
<tool file="emboss_5/emboss_wordmatch.xml" />
|
||||
</section>
|
||||
<label text="NGS Toolbox Beta" id="ngs" />
|
||||
<section name="NGS: QC and manipulation" id="cshl_library_information">
|
||||
|
||||
+10
-10
@@ -144,14 +144,14 @@
|
||||
<tool file="regVariation/t_test_two_samples.xml" />
|
||||
<tool file="regVariation/compute_q_values.xml" />
|
||||
<label text="GFF" id="gff" />
|
||||
<tool file="stats/count_gff_features.xml" />
|
||||
<tool file="stats/count_gff_features.xml" />
|
||||
</section>
|
||||
<!--
|
||||
Keep this section commented until all of the tools have functional tests
|
||||
<section name="Wavelet Analysis" id="dwt">
|
||||
<tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
|
||||
<tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
|
||||
<tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
|
||||
<tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
|
||||
<tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
|
||||
</section>
|
||||
-->
|
||||
@@ -184,8 +184,8 @@
|
||||
<tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
|
||||
<tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
|
||||
<tool file="regVariation/draw_stacked_barplots.xml" />
|
||||
<tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
|
||||
<tool file="regVariation/microsatellite_birthdeath.xml" />
|
||||
<tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
|
||||
<tool file="regVariation/microsatellite_birthdeath.xml" />
|
||||
</section>
|
||||
<section name="Multiple regression" id="multReg">
|
||||
<tool file="regVariation/linear_regression.xml" />
|
||||
@@ -241,7 +241,7 @@
|
||||
</section>
|
||||
<section name="NGS: QC and manipulation" id="NGS_QC">
|
||||
<label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
|
||||
<tool file="rgenetics/rgFastQC.xml" />
|
||||
<tool file="rgenetics/rgFastQC.xml" />
|
||||
<label text="Illumina fastq" id="illumina" />
|
||||
<tool file="fastq/fastq_groomer.xml" />
|
||||
<tool file="fastq/fastq_paired_end_splitter.xml" />
|
||||
@@ -280,21 +280,21 @@
|
||||
<tool file="fastx_toolkit/fastx_collapser.xml" />
|
||||
<tool file="fastx_toolkit/fastx_renamer.xml" />
|
||||
<tool file="fastx_toolkit/fastx_reverse_complement.xml" />
|
||||
<tool file="fastx_toolkit/fastx_trimmer.xml" />
|
||||
<tool file="fastx_toolkit/fastx_trimmer.xml" />
|
||||
</section>
|
||||
<section name="NGS: Picard (beta)" id="picard_beta">
|
||||
<label text="QC/Metrics for sam/bam" id="qcsambam"/>
|
||||
<tool file="picard/picard_BamIndexStats.xml" />
|
||||
<tool file="picard/rgPicardASMetrics.xml" />
|
||||
<tool file="picard/rgPicardGCBiasMetrics.xml" />
|
||||
<tool file="picard/rgPicardLibComplexity.xml" />
|
||||
<tool file="picard/rgPicardASMetrics.xml" />
|
||||
<tool file="picard/rgPicardGCBiasMetrics.xml" />
|
||||
<tool file="picard/rgPicardLibComplexity.xml" />
|
||||
<tool file="picard/rgPicardInsertSize.xml" />
|
||||
<tool file="picard/rgPicardHsMetrics.xml" />
|
||||
<label text="bam/sam Cleaning" id="picard-clean" />
|
||||
<tool file="picard/picard_AddOrReplaceReadGroups.xml" />
|
||||
<tool file="picard/picard_ReorderSam.xml" />
|
||||
<tool file="picard/picard_ReplaceSamHeader.xml" />
|
||||
<tool file="picard/rgPicardFixMate.xml" />
|
||||
<tool file="picard/rgPicardFixMate.xml" />
|
||||
<tool file="picard/rgPicardMarkDups.xml" />
|
||||
</section>
|
||||
<!--
|
||||
|
||||
+30
-30
@@ -4,19 +4,19 @@ import os,sys
|
||||
onoff = 1
|
||||
tool_list = []
|
||||
for line in open("tool_conf.xml.sample", "r"):
|
||||
if line.find("<!--") != -1:
|
||||
if line.find("<!--") != -1:
|
||||
onoff = 0
|
||||
if line.find("file") != -1 and onoff==1:
|
||||
strs = line.split('\"')
|
||||
if line.find("file") != -1 and onoff==1:
|
||||
strs = line.split('\"')
|
||||
tool_list.append(strs[1])
|
||||
if line.find("<section") != -1 and onoff==1:
|
||||
if line.find("<section") != -1 and onoff==1:
|
||||
keys = line.strip().split('\"')
|
||||
n = 0
|
||||
strtmp = "section::"
|
||||
while n < len(keys) :
|
||||
if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]
|
||||
if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-"
|
||||
n = n + 1
|
||||
while n < len(keys) :
|
||||
if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1]
|
||||
if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-"
|
||||
n = n + 1
|
||||
tool_list.append(strtmp.replace(' ', '_'))
|
||||
if line.find("-->") != -1:
|
||||
onoff =1
|
||||
@@ -26,42 +26,42 @@ name = []
|
||||
id = []
|
||||
desc = []
|
||||
tool_infos = []
|
||||
for tool in tool_list :
|
||||
if tool.find("section")!=-1 :
|
||||
for tool in tool_list :
|
||||
if tool.find("section")!=-1 :
|
||||
tool_info = dict()
|
||||
tool_info["id"] = tool
|
||||
tool_infos.append(tool_info)
|
||||
if os.path.exists("tools/"+tool) :
|
||||
for line in open("tools/"+tool) :
|
||||
if line.find("<tool ") != -1 and line.find("id") != -1 :
|
||||
keys = line.strip().split('\"')
|
||||
n = 0
|
||||
tool_info = dict()
|
||||
tool_info["desc"] = ''
|
||||
while n < len(keys) :
|
||||
if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_')
|
||||
if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1]
|
||||
if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1]
|
||||
n = n + 1
|
||||
tool_infos.append(tool_info)
|
||||
break
|
||||
if os.path.exists("tools/"+tool) :
|
||||
for line in open("tools/"+tool) :
|
||||
if line.find("<tool ") != -1 and line.find("id") != -1 :
|
||||
keys = line.strip().split('\"')
|
||||
n = 0
|
||||
tool_info = dict()
|
||||
tool_info["desc"] = ''
|
||||
while n < len(keys) :
|
||||
if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_')
|
||||
if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1]
|
||||
if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1]
|
||||
n = n + 1
|
||||
tool_infos.append(tool_info)
|
||||
break
|
||||
|
||||
flag=0
|
||||
if len(sys.argv) == 1 :
|
||||
for tool_info in tool_infos:
|
||||
if tool_info["id"].find("section") != -1 :
|
||||
if len(sys.argv) == 1 :
|
||||
for tool_info in tool_infos:
|
||||
if tool_info["id"].find("section") != -1 :
|
||||
print "==========================================================================================================================================="
|
||||
print "%-45s\t%-40s\t%s" % ("id", "name", tool_info["id"])
|
||||
print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"
|
||||
else :
|
||||
print "%-45s\t%-40s" % (tool_info["id"], tool_info["name"])
|
||||
else:
|
||||
for tool_info in tool_infos:
|
||||
else:
|
||||
for tool_info in tool_infos:
|
||||
if tool_info["id"].find("section") != -1 :
|
||||
flag=0
|
||||
elif flag==1:
|
||||
print " functional.test_toolbox:TestForTool_%s" % tool_info["id"],
|
||||
if tool_info["id"].replace('section::', '')==sys.argv[1]:
|
||||
if tool_info["id"].replace('section::', '')==sys.argv[1]:
|
||||
flag=1
|
||||
|
||||
#for key in tool_infos.keys():
|
||||
|
||||
Reference in New Issue
Block a user