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edited tiara.xml
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@Minamehr
Minamehr committed Oct 17, 2024
1 parent aa1e4d1 commit 408748c
Showing 1 changed file with 35 additions and 44 deletions.
79 changes: 35 additions & 44 deletions tools/tiara/tiara.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,11 @@
<expand macro="biotools"/>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
mkdir ./results/ &&
tiara
-t \${GALAXY_SLOTS:-4}
-i '$input'
-o '$output'
-o ./results/main_result.txt
#if $probabilities
--pr '$probabilities'
Expand All @@ -27,14 +28,13 @@
--k1 $advanced_options.advance.first_stage_kmer
--k2 $advanced_options.advance.second_stage_kmer
#end if
#if $taxonomy_filter
--tf
#for $tf in $taxonomy_filter
--tf #for $tf in $taxonomy_filter
$tf
#end for
#for $tf in $taxonomy_filter
&& mv ../outputs/${tf}*.dat ${tf}.fasta
&& ls -l ./results/
&& mv ./results/${tf}*.dat ./results/${tf}.fasta
#end for
#end if
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</section>
</inputs>
<outputs>
<data name="output" format="txt" label="${tool.name} on ${on_string}: sequence ID, classification results"/>
<collection name="output_fasta" type="list" label="${tool.name} on ${on_string}: classified sequences in Fasta Output">
<filter>taxonomy_filter</filter>
<discover_datasets pattern="__name_and_ext__" ext="fasta" />
<collection name="output" type="list" label="${tool.name} on ${on_string}: classified sequences in txt and Fasta Output">
<discover_datasets pattern="__name_and_ext__" ext="fasta,txt" directory="results" />
</collection>
</outputs>
<tests>
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<param name="input" value="plast_fr.fasta.gz"/>
<param name="taxonomy_filter" value="pla"/>
<output name="output" ftype="txt">
<assert_contents>
<has_text_matching expression=".*sequence_id*"/>
<has_n_lines n="11" delta="5"/>
</assert_contents>
</output>
<output_collection name="output" type="list">
<element name="main_result" file="main_result01.txt" ftype="txt"/>
<element name="pla" file="pla.fasta" ftype="fasta" />
</output_collection>
</test>
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<param name="input" value="mitplas1.fasta"/>
<param name="taxonomy_filter" value="pla,mit"/>
<output name="output" ftype="txt">
<assert_contents>
<has_text_matching expression=".*sequence_id*"/>
<has_n_lines n="30" delta="5"/>
</assert_contents>
</output>
<output_collection name="output" type="list">
<element name="main_result" file="main_result02.txt" ftype="txt" />
<element name="mit" file="mit" ftype="fasta" />
<element name="pla" file="pla" ftype="fasta" />
</output_collection>
</test>
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<param name="input" value="sample_all.fasta"/>
<param name="taxonomy_filter" value="euk,bac,arc"/>
<output name="output" ftype="txt">
<assert_contents>
<has_text_matching expression=".*sequence_id*"/>
<has_n_lines n="51" delta="5"/>
</assert_contents>
</output>
<output_collection name="output" type="list">
<element name="arc" file="arc" ftype="fasta" />
<element name="bac" file="bac" ftype="fasta" />
<element name="euk" file="euk" ftype="fasta" />
<element name="main_result" file="main_result03.txt" ftype="txt" />
</output_collection>
</test>
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<param name="input" value="eukarya_fr.fasta"/>
<param name="taxonomy_filter" value="euk"/>
<param name="min_len" value="5000"/>
<param name="cutoff_stage1" value="0.65"/>
<param name="cutoff_stage2" value="0.60"/>
<output name="output" ftype="txt">
<assert_contents>
<has_text_matching expression=".*sequence_id*"/>
<has_n_lines n="11" delta="5"/>
</assert_contents>
</output>
<output_collection name="output" type="list">
<element name="euk" file="euk" ftype="fasta" />
<element name="main_result" file="main_result04.txt" ftype="txt" />
</output_collection>
</test>
<test expect_num_outputs="2">
<test expect_num_outputs="1">
<param name="input" value="bacteria_fr.fasta"/>
<param name="taxonomy_filter" value="bac"/>
<param name="min_len" value="5000"/>
<param name="cutoff_stage1" value="0.65"/>
<param name="cutoff_stage2" value="0.60"/>
<param name="probabilities" value="true"/>
<output name="output" ftype="txt">
<assert_contents>
<has_text_matching expression=".*bac*"/>
<has_n_lines n="11" delta="5"/>
</assert_contents>
</output>
<output_collection name="output" type="list">
<element name="bac" file="bac" ftype="fasta" />
<element name="main_result" file="main_result05.txt" ftype="txt" />
</output_collection>
</test>
</tests>
<help><![CDATA[
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