| Previous changeset 21:a6dcb86af112 (2015-07-28) Next changeset 23:6e5c95760ab1 (2016-09-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 03f64004f90ac0a7be67ecfc355a7b361f3c3314 |
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modified:
README.rst htseq-count.xml |
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removed:
tool_dependencies.xml |
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| diff -r a6dcb86af112 -r 55ed198f2c1c README.rst --- a/README.rst Tue Jul 28 13:29:18 2015 -0400 +++ b/README.rst Tue Sep 20 17:51:06 2016 -0400 |
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| @@ -12,15 +12,8 @@ Installation directly from the `Galaxy Toolshed <http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count>`_ is recommended. -Development ------------ - -Repository-Maintainer: Lance Parsons <lparsons@princeton.edu> - -Repository-Development: `https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper <https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper>`_ - -License -------- +Galaxy Wrapper License +---------------------- Copyright (c) 2012-2014, Lance R. Parsons <lparsons@princeton.edu> All rights reserved. |
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| diff -r a6dcb86af112 -r 55ed198f2c1c htseq-count.xml --- a/htseq-count.xml Tue Jul 28 13:29:18 2015 -0400 +++ b/htseq-count.xml Tue Sep 20 17:51:06 2016 -0400 |
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| b'@@ -1,10 +1,8 @@\n-<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy1">\n+<tool id="htseq_count" name="htseq-count" version="0.6.1galaxy2">\n <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>\n <requirements>\n- <requirement type="package" version="0.6.1">htseq</requirement>\n- <requirement type="package" version="1.7.1">numpy</requirement>\n+ <requirement type="package" version="0.6.1.post1">htseq</requirement>\n <requirement type="package" version="0.1.19">samtools</requirement>\n- <requirement type="package" version="0.7.7">pysam</requirement>\n </requirements>\n \n <stdio>\n@@ -22,7 +20,7 @@\n <command><![CDATA[\n ##set up input files\n #set $reference_fasta_filename = "localref.fa"\n- #if $samout_conditional.samout:\n+ #if $samout_conditional.samout == "Yes":\n #if str( $samout_conditional.reference_source.reference_source_selector ) == "history":\n ln -s "${samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&\n samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&\n@@ -30,11 +28,11 @@\n #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )\n #end if\n #end if\n- #if $force_sort:\n+ #if $force_sort == "True":\n #if $samfile.extension == \'bam\':\n samtools sort -n "$samfile" "name_sorted_alignment" &&\n #else\n- samtools view -Su -t ${reference_fasta_filename}.fai "$samfile" | samtools sort -n - "name_sorted_alignment" &&\n+ samtools view -Su -t "${reference_fasta_filename}.fai" "$samfile" | samtools sort -n - "name_sorted_alignment" &&\n #end if\n #end if\n htseq-count\n@@ -43,10 +41,10 @@\n --minaqual=$minaqual\n --type="$featuretype"\n --idattr="$idattr"\n- #if $samout_conditional.samout:\n+ #if $samout_conditional.samout == "Yes":\n --samout=$__new_file_path__/${samoutfile.id}_tmp\n #end if\n- #if $force_sort:\n+ #if $force_sort == "True":\n --order=name\n --format=bam\n name_sorted_alignment.bam\n@@ -57,8 +55,8 @@\n #end if\n "$gfffile"\n | awk \'{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}\' > $counts 2>$othercounts\n- #if $samout_conditional.samout:\n- && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile\n+ #if $samout_conditional.samout == "Yes":\n+ && samtools view -Su -t "${reference_fasta_filename}.fai" "$__new_file_path__/${samoutfile.id}_tmp" | samtools sort -o - sorted > "$samoutfile"\n #end if\n ]]>\n </command>\n@@ -66,32 +64,34 @@\n <inputs>\n <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>\n <param format="gff" name="gfffile" type="data" label="GFF File"/>\n- <param name="mode" type="select" label="Mode" help="(--mode)">\n+ <param name="mode" type="select" label="Mode" argument="(--mode)">\n <help>Mode to handle reads overlapping more than one feature.</help>\n- <option value="union" selected="true">Union</option>\n+ <option value="union" selected="True">Union</option>\n <option value="intersection-strict">Intersection (strict)</option>\n <option value="intersection-nonempty">Intersection (nonempty)</option>\n </param>\n- <param name="stranded" type="select" label="Stranded" help="(--stranded)">\n+ <param name="stranded" type="select" label="Stranded" argument="(--stranded)">\n <help>Specify whether the data is from a strand-specific assay. \'Reverse\' means yes with reversed strand interpretation.</help>\n- <option value="yes" selected="true">Yes</option>\n+ <opti'..b'" type="select" label="Choose the source for the reference list">\n <option value="cached">Locally cached</option>\n@@ -110,6 +110,9 @@\n </when>\n </conditional>\n </when>\n+ <when value="No">\n+ <!-- Do nothing -->\n+ </when>\n </conditional>\n <param name="force_sort" type="boolean" value="False" truevalue="True" falsevalue="False" label="Force sorting of SAM/BAM file by NAME">\n <help>This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.</help>\n@@ -120,7 +123,7 @@\n <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>\n <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>\n <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">\n- <filter>samout_conditional[\'samout\']</filter>\n+ <filter>samout_conditional[\'samout\'] == "Yes"</filter>\n </data>\n </outputs>\n \n@@ -128,14 +131,14 @@\n <test>\n <param name="samfile" value="htseq-test.sam" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="False" />\n+ <param name="samout" value="No" />\n <output name="counts" file="htseq-test_counts.tsv" />\n <output name="othercounts" file="htseq-test_othercounts.tsv" />\n </test>\n <test>\n <param name="samfile" value="htseq-test.sam" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="False" />\n+ <param name="samout" value="No" />\n <param name="force_sort" value="True" />\n <output name="counts" file="htseq-test_counts.tsv" />\n <output name="othercounts" file="htseq-test_othercounts.tsv" />\n@@ -143,7 +146,7 @@\n <test>\n <param name="samfile" value="htseq-test.bam" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="False" />\n+ <param name="samout" value="No" />\n <output name="counts" file="htseq-test_counts.tsv" />\n <output name="othercounts" file="htseq-test_othercounts.tsv" />\n </test>\n@@ -151,7 +154,7 @@\n <param name="samfile" value="htseq-test-paired.bam" />\n <param name="singlepaired" value="paired" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="False" />\n+ <param name="samout" value="No" />\n <output name="counts" file="htseq-test-paired_counts.tsv" />\n <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />\n </test>\n@@ -159,7 +162,7 @@\n <param name="samfile" value="htseq-test-paired.bam" />\n <param name="singlepaired" value="paired" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="False" />\n+ <param name="samout" value="No" />\n <param name="force_sort" value="True" />\n <output name="counts" file="htseq-test-paired_counts.tsv" />\n <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />\n@@ -294,7 +297,7 @@\n year = {2015},\n pmid = {25260700},\n pages = {166--169},\n- file = {Full Text PDF:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/84XQB8V6/Anders et al. - 2015 - HTSeq\xe2\x80\x94a Python framework to work with high-through.pdf:application/pdf;Snapshot:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/JKUAUCKB/166.html:text/html}\n+ }\n }\n </citation>\n </citations>\n' |
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| diff -r a6dcb86af112 -r 55ed198f2c1c tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 28 13:29:18 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - - <package name="samtools" version="0.1.19"> - <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="pysam" version="0.7.7"> - <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="numpy" version="1.7.1"> - <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="htseq" version="0.6.1"> - <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - -</tool_dependency> |