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gfastats linting fixes #1560

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gfastats linting fixes #1560

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ed33b57
text is txt
bernt-matthias Dec 14, 2024
844a054
fix test
bernt-matthias Dec 14, 2024
da1d265
forbid fastq
bernt-matthias Dec 14, 2024
244544d
bump
bernt-matthias Dec 14, 2024
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8 changes: 4 additions & 4 deletions tools/gfastats/gfastats.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@
]]></command>
<inputs>
<param name="input_file" argument="--fasta" type="data"
format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz"
format="fasta,fastqsanger,gfa1,fasta.gz,fastqsanger.gz,gfa1.gz"
label="Input file"/>
<conditional name="target_condition">
<param name="target_option" type="select" label="Specify target sequences">
Expand Down Expand Up @@ -111,7 +111,7 @@
</param>
<when value="manipulation">
<param argument="--swiss-army-knife" type="data"
format="text" label="SAK input file" optional="true"
format="txt" label="SAK input file" optional="true"
help="Set of instructions provided as an ordered list"/>
<conditional name="output_condition">
<param argument="--out-format" type="select"
Expand Down Expand Up @@ -201,7 +201,7 @@
<data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
<filter>mode_condition['selector'] == 'statistics'</filter>
<change_format>
<when input="tabular" value="false" format="text"/>
<when input="tabular" value="false" format="txt"/>
</change_format>
</data>
<data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">
Expand Down Expand Up @@ -247,7 +247,7 @@
<test expect_num_outputs="1">
<param name="input_file" value="dataset_01.fastq.gz"/>
<conditional name="target_condition">
<param name="target_condition" value="true"/>
<param name="target_option" value="true"/>
<param name="target_sequence" value="S1_1"/>
</conditional>
<conditional name="mode_condition">
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2 changes: 1 addition & 1 deletion tools/gfastats/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">1.3.9</token>
<token name="@SUFFIX_VERSION@">0</token>
<token name="@SUFFIX_VERSION@">1</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">gfastats</requirement>
Expand Down
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