| Previous changeset 7:6b87499054f6 (2017-09-14) Next changeset 9:c3ce472a315f (2017-09-26) |
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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b4991fb40364a975d0ea782035b930874c57665c |
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modified:
dr-disco_bam-extract.xml dr-disco_classify.xml dr-disco_detect.xml dr-disco_fix.xml dr-disco_integrate.xml macros.xml |
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| diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_bam-extract.xml --- a/dr-disco_bam-extract.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/dr-disco_bam-extract.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0"> +<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@"> <description>Extracts reads from two targeted regions</description> <macros> |
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| diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_classify.xml --- a/dr-disco_classify.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/dr-disco_classify.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@-g0"> +<tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@"> <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description> <macros> |
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| diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_detect.xml --- a/dr-disco_detect.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/dr-disco_detect.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@-g0"> +<tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@"> <description>Detects break-points in RNA-seq</description> <macros> <import>macros.xml</import> @@ -15,7 +15,7 @@ '${output_fusion_events}' ]]></command> <inputs> - <param name="star_discordant_alignment_fixed" type="data" format="tabular" label="Discordant alignment file of STAR (processed with dr-disco fix)" /> + <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" /> <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0" label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." /> </inputs> |
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| diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_fix.xml --- a/dr-disco_fix.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/dr-disco_fix.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0"> +<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@"> <description>Fixes chimeric alignments from STAR</description> <macros> <import>macros.xml</import> |
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| diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_integrate.xml --- a/dr-disco_integrate.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/dr-disco_integrate.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -1,9 +1,9 @@ -<tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@-g0"> +<tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@"> <description>Merges corresponding genomic breaks and exon-to-exon junctions</description> <macros> <import>macros.xml</import> </macros> - + <expand macro="requirements"/> <expand macro="version_command"/> @@ -11,7 +11,7 @@ dr-disco integrate #if $gtf: - --gtf ${gtf} + --gtf '${gtf}' #end if '${dr_disco_classify_output}' |
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| diff -r 6b87499054f6 -r 922b52cf9b35 macros.xml --- a/macros.xml Thu Sep 14 06:24:47 2017 -0400 +++ b/macros.xml Thu Sep 14 08:35:12 2017 -0400 |
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| @@ -5,8 +5,8 @@ <yield/> </requirements> </xml> - - <token name="@TOOL_VERSION@">0.10.0-g2</token> + + <token name="@TOOL_VERSION@">0.10.0-g3</token> <xml name="version_command"> <version_command>dr-disco --version | head -n 1</version_command> |