| Previous changeset 7:02f09108bcff (2018-04-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be |
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modified:
damidseq_core.xml test-data/output_ratio.bed test-data/output_ratio_full.bed |
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added:
test-data/control2.bam test-data/fusion2.bam test-data/output_ratio2.gff test-data/output_ratio_full2.gff |
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| diff -r 02f09108bcff -r 621837e9bfed damidseq_core.xml --- a/damidseq_core.xml Fri Apr 20 06:25:32 2018 -0400 +++ b/damidseq_core.xml Thu May 03 05:12:02 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="damidseq_core" name="damidseq" version="0.1.4"> +<tool id="damidseq_core" name="damidseq" version="0.1.5"> <description>align, extend and normalize a DamID-seq experiment</description> <requirements> <requirement type="package" version="1.4">damidseq_pipeline</requirement> @@ -30,14 +30,17 @@ --qscore1min=$qscore1min --qscore2max=$qscore2max --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' && - mv Fusion-vs-Dam.gatc.* gatc.output + #set EXT = "-ext%s" % $len if $extend_reads == '1' else "" + mv 'Dam-${dam.element_identifier}${EXT}.bam' '$control_output' && + mv '${dam_fusion.element_identifier}${EXT}.bam' '$fusion_output' && + mv '${dam_fusion.element_identifier}-vs-Dam.gatc.$output_format' gatc.output #if str($full_data_files): - && mv Fusion-vs-Dam.* full.output + && mv '${dam_fusion.element_identifier}-vs-Dam.$output_format' full.output #end if ]]></command> <configfiles> - <configfile name="index">A1 Dam -A2 Fusion</configfile> + <configfile name="index">A1 Dam-$dam.element_identifier +A2 $dam_fusion.element_identifier</configfile> </configfiles> <inputs> <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> @@ -75,7 +78,7 @@ <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/> </inputs> <outputs> - <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}"> + <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}" default_identifier_source="dam_fusion"> <change_format> <when input="output_format" value="gff" format="gff" /> </change_format> @@ -88,7 +91,7 @@ </action> </actions> </data> - <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}"> + <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}" default_identifier_source="dam_fusion"> <filter>full_data_files</filter> <change_format> <when input="output_format" value="gff" format="gff" /> @@ -102,7 +105,7 @@ </action> </actions> </data> - <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment on ${on_string}"> + <data name="control_output" format="bam" label="Dam-only alignment on ${on_string}" default_identifier_source="dam_fusion"> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> @@ -112,7 +115,7 @@ </action> </actions> </data> - <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment on ${on_string}"> + <data name="fusion_output" format="bam" label="Dam-fusion alignment on ${on_string}" default_identifier_source="dam_fusion"> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> @@ -135,6 +138,7 @@ <output name="fusion_output" file="fusion.bam"/> </test> <test> + <!-- test full data output --> <param name="dam" value="A001.fastq"/> <param name="dam_fusion" value="A002.fastq"/> <param name="gatc_frag_file" value="dm6.GATC.gff"/> @@ -146,6 +150,21 @@ <output name="control_output" file="control.bam"/> <output name="fusion_output" file="fusion.bam"/> </test> + <test> + <!-- test no extension and gff outpt --> + <param name="dam" value="A001.fastq"/> + <param name="dam_fusion" value="A002.fastq"/> + <param name="gatc_frag_file" value="dm6.GATC.gff"/> + <param name="reference_index" value="dm6"/> + <param name="norm_method" value="rpm"/> + <param name="full_data_files" value="true"/> + <param name="extend_reads" value="false"/> + <param name="output_format" value="gff"/> + <output name="output_ratio" file="output_ratio2.gff"/> + <output name="output_ratio_full" file="output_ratio_full2.gff"/> + <output name="control_output" file="control2.bam"/> + <output name="fusion_output" file="fusion2.bam"/> + </test> </tests> <help><![CDATA[ |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/control2.bam |
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| Binary file test-data/control2.bam has changed |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/fusion2.bam |
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| Binary file test-data/fusion2.bam has changed |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/output_ratio.bed --- a/test-data/output_ratio.bed Fri Apr 20 06:25:32 2018 -0400 +++ b/test-data/output_ratio.bed Thu May 03 05:12:02 2018 -0400 |
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| @@ -1,3 +1,3 @@ -track type=bedGraph name="Fusion-vs-Dam" description="Fusion DamIDseq" +track type=bedGraph name="A002.fastq-vs-Dam" description="A002.fastq DamIDseq" X 159 366 0 X 366 501 0 |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/output_ratio2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ratio2.gff Thu May 03 05:12:02 2018 -0400 |
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| @@ -0,0 +1,2 @@ +X . . 159 366 0 . . . +X . . 366 501 0 . . . |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/output_ratio_full.bed --- a/test-data/output_ratio_full.bed Fri Apr 20 06:25:32 2018 -0400 +++ b/test-data/output_ratio_full.bed Thu May 03 05:12:02 2018 -0400 |
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| @@ -1,4 +1,4 @@ -track type=bedGraph name="Fusion-vs-Dam" description="Fusion DamIDseq" +track type=bedGraph name="A002.fastq-vs-Dam" description="A002.fastq DamIDseq" X 0 74 0 X 75 149 0 X 150 224 0 |
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| diff -r 02f09108bcff -r 621837e9bfed test-data/output_ratio_full2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ratio_full2.gff Thu May 03 05:12:02 2018 -0400 |
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| @@ -0,0 +1,15 @@ +X . . 0 74 0 . . . +X . . 75 149 0 . . . +X . . 150 224 0 . . . +X . . 225 299 0 . . . +X . . 300 374 0 . . . +X . . 375 449 0 . . . +X . . 450 524 0 . . . +X . . 525 599 0 . . . +X . . 600 674 0 . . . +X . . 675 749 0 . . . +X . . 750 824 0 . . . +X . . 825 899 0 . . . +X . . 900 974 0 . . . +X . . 975 1049 0 . . . +X . . 1050 1124 0 . . . |