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jmchiltonjmchilton
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Remove stdio from generated tools - just use exit_code for everything.
Other small formatting tweaks - but less than #674 since I'm trying to keep these tools the way they are when tool_init generates them - at least for those options. This also doesn't strip stdio from other places like the bwa test tool that broke the tests in #674.
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‎docs/_writing_intro.rst‎

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@@ -53,7 +53,7 @@ definitions for the input and output as well as an actual command template.
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.. literalinclude:: writing/seqtk_seq_v2.xml
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:language: xml
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:emphasize-lines: 8-16
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:emphasize-lines: 5-13
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.. include:: _writing_from_help_command.rst
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.. literalinclude:: writing/seqtk_seq_v3.xml
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:language: xml
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:emphasize-lines: 17-58
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:emphasize-lines: 14-55
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.. include:: _writing_lint_intro.rst
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‎docs/_writing_parameters.rst‎

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@@ -50,7 +50,7 @@ At this point the tool would look like:
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.. literalinclude:: writing/seqtk_seq_v4.xml
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:language: xml
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:emphasize-lines: 10-13,17-23
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:emphasize-lines: 7-10,14-20
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Conditional Parameters
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.. literalinclude:: writing/seqtk_seq_v5.xml
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:language: xml
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:emphasize-lines: 13-19,31-43
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:emphasize-lines: 10-16,28-40
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For tools like this where there are many options but in the most uses the defaults
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are preferred - a common idiom is to break the parameters into simple and
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.. literalinclude:: writing/seqtk_seq_v6.xml
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:language: xml
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:emphasize-lines: 10-21,26-33,54-55
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:emphasize-lines: 7-18,23-30,51-52

‎docs/_writing_suites.rst‎

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@@ -30,7 +30,7 @@ This will produce the two files in your current directory instead of just one
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.. literalinclude:: writing/seqtk_seq_with_macros.xml
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:language: xml
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:emphasize-lines: 2-6,46
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:emphasize-lines: 2-5,45
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.. literalinclude:: writing/seqtk_macros.xml
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:language: xml

‎docs/writing/gen.sh‎

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@@ -5,15 +5,15 @@ mv seqtk_seq.xml seqtk_seq_v1.xml
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planemo tool_init --force \
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--id 'seqtk_seq' \
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--name 'Convert to FASTA (seqtk)' \
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--requirement seqtk@1.0-r68 \
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--requirement seqtk@1.2 \
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--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
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--example_input 2.fastq \
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--example_output 2.fasta
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mv seqtk_seq.xml seqtk_seq_v2.xml
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planemo tool_init --force \
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--id 'seqtk_seq' \
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--name 'Convert to FASTA (seqtk)' \
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--requirement seqtk@1.0-r68 \
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--requirement seqtk@1.2 \
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--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
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--example_input 2.fastq \
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--example_output 2.fasta \

‎docs/writing/seqtk_macros.xml‎

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<yield/>
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</requirements>
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</xml>
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<xml name="stdio">
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<stdio>
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<exit_code range="1:" />
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</stdio>
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</xml>
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<xml name="citations">
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<citations>
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<yield />
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</citations>
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</xml>
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</macros>
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</macros>

‎docs/writing/seqtk_seq_v1.xml‎

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<tool id="seqtk_seq" name="Convert to FASTA (seqtk)" version="0.1.0">
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<requirements>
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</requirements>
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<stdio>
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<exit_code range="1:" />
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</stdio>
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<command><![CDATA[
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<command detect_errors="exit_code"><![CDATA[
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TODO: Fill in command template.
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]]></command>
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<inputs>

‎docs/writing/seqtk_seq_v2.xml‎

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<requirements>
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<requirement type="package" version="1.2">seqtk</requirement>
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</requirements>
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<stdio>
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<exit_code range="1:" />
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</stdio>
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<command><![CDATA[
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<command detect_errors="exit_code"><![CDATA[
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seqtk seq -a "$input1" > "$output1"
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]]></command>
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<inputs>

‎docs/writing/seqtk_seq_v3.cwl‎

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class: CommandLineTool
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id: "seqtk_seq"
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label: "Convert to FASTA (seqtk)"
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requirements:
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hints:
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- class: DockerRequirement
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dockerPull: dukegcb/seqtk
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inputs:

‎docs/writing/seqtk_seq_v3.xml‎

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<requirements>
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<requirement type="package" version="1.2">seqtk</requirement>
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</requirements>
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<stdio>
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<exit_code range="1:" />
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</stdio>
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<command><![CDATA[
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<command detect_errors="exit_code"><![CDATA[
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seqtk seq -a "$input1" > "$output1"
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]]></command>
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<inputs>

‎docs/writing/seqtk_seq_v4.xml‎

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<requirements>
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<requirement type="package" version="1.2">seqtk</requirement>
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</requirements>
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<stdio>
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<exit_code range="1:" />
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</stdio>
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<command><![CDATA[
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<command detect_errors="exit_code"><![CDATA[
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seqtk seq
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$shift_quality
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-q $quality_min

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