| Previous changeset 1:0632744d5a5f (2020-05-23) Next changeset 3:a95960a63220 (2020-06-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c" |
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modified:
consensus.xml macros.xml tool_data_table_conf.xml.sample |
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added:
test-data/variants.vcf.gz |
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| diff -r 0632744d5a5f -r 12c40c8c86db consensus.xml --- a/consensus.xml Sat May 23 13:37:18 2020 -0400 +++ b/consensus.xml Thu May 28 02:38:54 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>Assembly polishing via neural networks</description> <macros> <import>macros.xml</import> @@ -6,45 +6,45 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ - ## initialize - ln -s '${bam}' 'alignment.bam' && - ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' && +## initialize +ln -s '${bam}' alignment.bam && +ln -s '${bam.metadata.bam_index}' alignment.bam.bai && - ## run - medaka consensus - ## optional - --debug ## increase log level - --threads \${GALAXY_SLOTS:-4} - --batch_size $batch_size - #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed' - --regions - #if $regions_cond.regions_sel == 'custom' - '$regions_cond.custom' - #else if $regions_cond.regions_sel == 'bed' - '$regions_cond.bed' - #end if - #end if - --chunk_len $chunk_len - --chunk_ovlp $chunk_ovlp - --model '$model' - $disable_cudnn - $check_output - $save_features - #if $RG - --RG '$RG' - #end if - #if $tag_name - --tag_name '$tag_name' - #end if - #if $tag_value - --tag_value $tag_value - #end if - $tag_keep_missing - ## required - 'alignment.bam' ## bam - 'result.hdf' ## output +## run +medaka consensus +## optional +--debug ## increase log level +--threads \${GALAXY_SLOTS:-4} +--batch_size $batch_size +#if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed' + --regions + #if $regions_cond.regions_sel == 'custom' + '$regions_cond.custom' + #else if $regions_cond.regions_sel == 'bed' + '$regions_cond.bed' + #end if +#end if +--chunk_len $chunk_len +--chunk_ovlp $chunk_ovlp +--model $model +$disable_cudnn +$check_output +$save_features +#if $RG + --RG '$RG' +#end if +#if $tag_name + --tag_name '$tag_name' +#end if +#if str($tag_value): + --tag_value $tag_value +#end if +$tag_keep_missing +## required +alignment.bam ## bam +'$out_result' ## output - |& tee 'log.txt' +|& tee '$out_log' ]]></command> <inputs> <param argument="bam" type="data" format="bam" label="Select input alignment"/> @@ -56,13 +56,13 @@ <option value="custom">Custom input</option> <option value="bed">BED file</option> </param> + <when value="none"/> <when value="custom"> - <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/> + <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/> </when> <when value="bed"> - <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/> + <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/> </when> - <when value="none"/> </conditional> <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/> <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/> @@ -80,11 +80,11 @@ </inputs> <outputs> <!-- standard --> - <data name="out_result" format="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result"> + <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result"> <filter>'result' in out</filter> </data> <!-- optional --> - <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"> + <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> <filter>'log' in out</filter> </data> </outputs> |
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| diff -r 0632744d5a5f -r 12c40c8c86db macros.xml --- a/macros.xml Sat May 23 13:37:18 2020 -0400 +++ b/macros.xml Thu May 28 02:38:54 2020 -0400 |
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| @@ -22,20 +22,20 @@ </citations> </xml> - <!-- + <!-- command --> - <token name="@REF_FASTA@"><![CDATA[ + <token name="@REF_FASTA@"><![CDATA[ #if $reference_source.reference_source_selector == 'history': - ln -f -s '$reference_source.ref_file' 'reference.fa' && + ln -f -s '$reference_source.ref_file' reference.fa && #else: - ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' && + ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if ]]></token> <!-- - input + input --> <xml name="b" token_argument="-b"> |
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| diff -r 0632744d5a5f -r 12c40c8c86db test-data/variants.vcf.gz |
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| Binary file test-data/variants.vcf.gz has changed |
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| diff -r 0632744d5a5f -r 12c40c8c86db tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sat May 23 13:37:18 2020 -0400 +++ b/tool_data_table_conf.xml.sample Thu May 28 02:38:54 2020 -0400 |
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| @@ -4,4 +4,4 @@ <columns>value, dbkey, name, path</columns> <file path="all_fasta.loc" /> </table> -</tables> \ No newline at end of file +</tables> |