Mercurial > repos > mvdbeek > damidseq_core
changeset 6:9b13b8bda9d8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549
| author | mvdbeek |
|---|---|
| date | Fri, 20 Apr 2018 06:14:00 -0400 |
| parents | 6c00620084a5 |
| children | 02f09108bcff |
| files | damidseq_core.xml test-data/output_ratio_full.bed |
| diffstat | 2 files changed, 28 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/damidseq_core.xml Wed Apr 18 15:02:42 2018 -0400 +++ b/damidseq_core.xml Fri Apr 20 06:14:00 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="damidseq_core" name="damidseq" version="0.1.3"> +<tool id="damidseq_core" name="damidseq" version="0.1.4"> <description>align, extend and normalize a DamID-seq experiment</description> <requirements> <requirement type="package" version="1.4">damidseq_pipeline</requirement> @@ -30,7 +30,10 @@ --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.* fusion.output + mv Fusion-vs-Dam.gatc.* gatc.output + #if str($full_data_files): + && mv Fusion-vs-Dam.* full.output + #end if ]]></command> <configfiles> <configfile name="index">A1 Dam @@ -55,7 +58,7 @@ <option value="gatc">To nearest GATC site</option> <option value="full">Full</option> </param> - <param argument="--full_data_files" type="boolean" truevalue="--full_data_file" falsevalue="" label="Output full binned ratio files (not only GATC array)"/> + <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/> <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/> <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/> <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/> @@ -72,7 +75,7 @@ <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="bed" from_work_dir="fusion.output" label="Dam-fusion vs Dam-only ratio"> + <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}"> <change_format> <when input="output_format" value="gff" format="gff" /> </change_format> @@ -85,7 +88,11 @@ </action> </actions> </data> - <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment"> + <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}"> + <filter>full_data_files == '--full_data_files'</filter> + <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"> @@ -95,7 +102,17 @@ </action> </actions> </data> - <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 on ${on_string}"> + <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 on ${on_string}"> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> @@ -123,7 +140,9 @@ <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"/> <output name="output_ratio" file="output_ratio.bed"/> + <output name="output_ratio_full" file="output_ratio_full.bed"/> <output name="control_output" file="control.bam"/> <output name="fusion_output" file="fusion.bam"/> </test>