Mercurial > repos > mvdbeek > damidseq_core
changeset 1:0d1514ecd757 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e
| author | mvdbeek |
|---|---|
| date | Thu, 23 Mar 2017 10:55:41 -0400 |
| parents | eb3a145c4962 |
| children | 69e346fb52a0 |
| files | damidseq_core.xml test-data/bt2/.GATC.gff test-data/output_ratio.bed test-data/output_ratio.bedgraph |
| diffstat | 4 files changed, 44 insertions(+), 22 deletions(-) [+] |
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--- a/damidseq_core.xml Wed Mar 22 09:56:09 2017 -0400 +++ b/damidseq_core.xml Thu Mar 23 10:55:41 2017 -0400 @@ -1,15 +1,14 @@ -<tool id="damidseq_core" name="damidseq" version="0.1.0"> - <description>align, extend and normalize a DAMID-seq experiment</description> +<tool id="damidseq_core" name="damidseq" version="0.1.1"> + <description>align, extend and normalize a DamID-seq experiment</description> <requirements> <requirement type="package" version="1.4">damidseq_pipeline</requirement> </requirements> <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command> <command detect_errors="aggressive"><![CDATA[ - export HOME="\$PWD" && - ln -f -s '$dam' A001.$dam.ext && - ln -f -s '$dam_fusion' A002.$dam_fusion.ext && + ln -f -s '$dam' A001.fastq && + ln -f -s '$dam_fusion' A002.fastq && ln -f -s '$index' index.txt && - damidseq_pipeline + HOME="\$PWD" damidseq_pipeline --bins=$bins --bowtie=1 --bowtie2_genome_dir='$reference_index.fields.path' @@ -28,16 +27,16 @@ --qscore1max=$qscore1max --qscore1min=$qscore1min --qscore2max=$qscore2max - --threads=\${GALAXY_SLOTS:-4} && - mv Fusion-vs-Dam.*.$output_format fusion.output + --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' && + mv Fusion-vs-Dam.* fusion.output ]]></command> <configfiles> <configfile name="index">A1 Dam A2 Fusion</configfile> </configfiles> <inputs> - <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control DAM alignment file"/> - <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion alignment file"/> + <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> + <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion fastq"/> <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="bowtie2_indexes"> <filter type="sort_by" column="2"/> @@ -46,7 +45,7 @@ </param> <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/> <param name="output_format" type="select" label="Select the output format for the peaks"> - <option value="bedgraph">Bedgraph</option> + <option value="bedgraph">Bed</option> <option value="gff">GFF</option> </param> <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/> @@ -71,22 +70,48 @@ <param argument="--qscore2max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from fusion-protein array"/> </inputs> <outputs> - <data name="output_ratio" format="bedgraph" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio"> + <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio"> <change_format> <when input="output_format" value="gff" format="gff" /> </change_format> + <actions> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_index" column="0"/> + </option> + </action> + </actions> </data> - <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment"/> - <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment"/> + <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment"> + <actions> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_index" column="0"/> + </option> + </action> + </actions> + </data> + <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment"> + <actions> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="reference_index" column="0"/> + </option> + </action> + </actions> + </data> </outputs> <tests> <test> <param name="dam" value="A001.fastq"/> <param name="dam_fusion" value="A002.fastq"/> <param name="gatc_frag_file" value="dm6.GATC.gff"/> - <param name="index" value="dm6"/> + <param name="reference_index" value="dm6"/> <param name="norm_method" value="rpm"/> - <output name="output_ratio" file="output_ratio.bedgraph"/> + <output name="output_ratio" file="output_ratio.bed"/> <output name="control_output" file="control.bam"/> <output name="fusion_output" file="fusion.bam"/> </test>
--- a/test-data/bt2/.GATC.gff Wed Mar 22 09:56:09 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -X . . 157 161 1 + . . -X . . 364 368 1 + . . -X . . 499 503 1 + . .