Mercurial > repos > bgruening > alevin
changeset 14:c9944a2600f1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
| author | bgruening |
|---|---|
| date | Mon, 18 Mar 2024 09:36:09 +0000 |
| parents | e32b215b7c04 |
| children | b8f3b923d066 |
| files | alevin.xml macros.xml |
| diffstat | 2 files changed, 41 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/alevin.xml Fri Jun 23 17:03:24 2023 +0000 +++ b/alevin.xml Mon Mar 18 09:36:09 2024 +0000 @@ -3,6 +3,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir ./index @@ -269,7 +270,13 @@ <param name="freqThreshold" value="5"/> <param name="dumpMtx" value="true"/> </section> - <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/> + <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx"> + <assert_contents> + <has_text text="MatrixMarket" /> + <has_n_columns n="5" /> + <has_n_lines n="105" /> + </assert_contents> + </output> </test> <test expect_num_outputs="11"> <conditional name="refTranscriptSource"> @@ -296,7 +303,13 @@ <param name="freqThreshold" value="5"/> <param name="dumpMtx" value="true"/> </section> - <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/> + <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" > + <assert_contents> + <has_text text="MatrixMarket" /> + <has_n_columns n="5" /> + <has_n_lines n="105" /> + </assert_contents> + </output> </test> <test expect_num_outputs="8"> <conditional name="refTranscriptSource"> @@ -323,7 +336,13 @@ <param name="freqThreshold" value="5"/> <param name="dumpMtx" value="true"/> </section> - <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/> + <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" compare="sim_size" ftype="mtx"> + <assert_contents> + <has_text text="MatrixMarket" /> + <has_n_columns n="5" /> + <has_n_lines n="105" /> + </assert_contents> + </output> </test> <test expect_num_outputs="14"> <conditional name="refTranscriptSource"> @@ -347,7 +366,13 @@ <section name="optional"> <param name="dumpMtx" value="true"/> </section> - <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/> + <output name="quants_mat_mtx" file="alevin_mat.mtx" compare="sim_size" ftype="mtx"> + <assert_contents> + <has_text text="MatrixMarket" /> + <has_n_columns n="5" /> + <has_n_lines n="17" /> + </assert_contents> + </output> <output name="salmon_quant_log" ftype="txt"> <assert_contents> <has_text text="Index contained 322 targets"/> @@ -363,7 +388,7 @@ <output_collection name="umigraphs" type="list" count="14"> <element name="AGTGGGATCTTAACCT"> <assert_contents> - <has_size value="4017" delta="1000"/> + <has_size value="4661" delta="1000"/> </assert_contents> </element> </output_collection>
--- a/macros.xml Fri Jun 23 17:03:24 2023 +0000 +++ b/macros.xml Mon Mar 18 09:36:09 2024 +0000 @@ -1,8 +1,13 @@ <macros> <token name="@TOOL_VERSION@">1.10.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@IDX_VERSION@">q7</token> <token name="@PROFILE_VERSION@">20.01</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">salmon</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">salmon</requirement> @@ -121,9 +126,10 @@ label="Discard orphan quasi" help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/> <conditional name="validmap"> - <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False" - label="Validate mappings" - help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/> + <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."> + <option value="--validateMappings">True</option> + <option value="" selected="true">False</option> + </param> <when value="--validateMappings"> <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99" label="Min Score Fraction" @@ -390,7 +396,7 @@ #end if ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext && ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext && - #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved': + #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved': #if $quant_type.input.single_or_paired.input_1.ext == 'fasta': #set $ext = 'fasta' #else: