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update minced, it was never published #1332

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update minced, it was never published #1332

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a0c7c08
update minced, it was never published
bgruening Sep 16, 2023
e0454df
Update minced.xml
bgruening Sep 16, 2023
6ebdf52
Update minced.xml
bgruening Sep 16, 2023
518be25
Update minced.xml
bgruening Sep 16, 2023
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20 changes: 7 additions & 13 deletions tools/minced/minced.xml
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Original file line number Diff line number Diff line change
@@ -1,16 +1,11 @@
<tool id="minced" name="detect CRISPR sequences" version="0.2.0">
<tool id="minced" name="detect CRISPR sequences" version="0.2.0" profile="22.05">
<description>(minced)</description>
<parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="250" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
<requirements>
<requirement type="package" version="0.2.0">minced</requirement>
</requirements>
<stdio>
<exit_code range=":-1" level="fatal" />
<exit_code range="1:" level="fatal" />
</stdio>
<command>
<command detect_errors="aggressive">>
<![CDATA[
temp_output=\$(mktemp);
touch ./temp_out.txt &&
minced
-minNR $minNR
-minRL $minRL
Expand All @@ -21,7 +16,7 @@
-searchWL $searchWL
#end if
$input
\$temp_output
./temp_out.txt
#if '-spacers' in str($outputs).split():
-spacers
#end if
Expand All @@ -31,11 +26,11 @@
#if '-gff' in str($outputs).split():
-gff
#end if
;
&&
python '$__tool_directory__/reformat.py' ./temp_out.txt results.bed results.tab

python $__tool_directory__/reformat.py \$temp_output results.bed results.tab;
#if '-spacers' in str($outputs).split():
mv \$temp_output'_spacers.fa' $output_fasta;
&& mv ./temp/_spacers.fa $output_fasta
#end if
]]>
</command>
Expand Down Expand Up @@ -118,4 +113,3 @@ If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.c
<citation type="doi">10.1186/1471-2105-8-209 </citation>
</citations>
</tool>